2018-10-08 23:22:42 transfer the raw fastq files to ubam format for gatk4 pipeline, for more detail information please see the log1 and log2 file. 2018-10-08 23:26:20 the transfer step is finished. 2018-10-08 23:26:20 the preprocessing step is start, for more detail information please see the log3 and log4 file. 2018-10-09 00:44:01 the preprocessing step is finished. 2018-10-09 00:44:01 the mutect2 step is start. [2018-10-09 00:44:05,57] [info] Running with database db.url = jdbc:hsqldb:mem:37f9fd7b-7b31-4b40-887f-68333c4d0ae9;shutdown=false;hsqldb.tx=mvcc [2018-10-09 00:44:14,60] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 [2018-10-09 00:44:14,62] [info] [RenameWorkflowOptionsInMetadata] 100% [2018-10-09 00:44:14,70] [info] Running with database db.url = jdbc:hsqldb:mem:c1023f52-d47f-4446-aec9-410425a8fa3b;shutdown=false;hsqldb.tx=mvcc [2018-10-09 00:44:15,10] [info] Slf4jLogger started [2018-10-09 00:44:15,49] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-51fd2ea", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2018-10-09 00:44:15,53] [info] Metadata summary refreshing every 2 seconds. [2018-10-09 00:44:15,56] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2018-10-09 00:44:15,56] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2018-10-09 00:44:15,56] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2018-10-09 00:44:16,55] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2018-10-09 00:44:16,57] [info] SingleWorkflowRunnerActor: Version 34 [2018-10-09 00:44:16,58] [info] SingleWorkflowRunnerActor: Submitting workflow [2018-10-09 00:44:16,62] [info] Unspecified type (Unspecified version) workflow ec34099b-7f45-4a33-b205-0cd6011f53f0 submitted [2018-10-09 00:44:16,67] [info] SingleWorkflowRunnerActor: Workflow submitted ec34099b-7f45-4a33-b205-0cd6011f53f0 [2018-10-09 00:44:16,67] [info] 1 new workflows fetched [2018-10-09 00:44:16,67] [info] WorkflowManagerActor Starting workflow ec34099b-7f45-4a33-b205-0cd6011f53f0 [2018-10-09 00:44:16,68] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData [2018-10-09 00:44:16,70] [warn] Couldn't find a suitable DSN, defaulting to a Noop one. [2018-10-09 00:44:16,71] [info] Using noop to send events. [2018-10-09 00:44:16,73] [info] WorkflowManagerActor Successfully started WorkflowActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [2018-10-09 00:44:16,73] [info] Retrieved 1 workflows from the WorkflowStoreActor [2018-10-09 00:44:16,73] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2018-10-09 00:44:16,74] [info] MaterializeWorkflowDescriptorActor [ec34099b]: Parsing workflow as WDL draft-2 [2018-10-09 00:44:21,94] [info] MaterializeWorkflowDescriptorActor [ec34099b]: Call-to-Backend assignments: Mutect2.CollectSequencingArtifactMetrics -> Local, Mutect2.FilterAlignmentArtifacts -> Local, Mutect2.CalculateContamination -> Local, Mutect2.Funcotate -> Local, Mutect2.M2 -> Local, Mutect2.FilterByOrientationBias -> Local, Mutect2.MergeBamOuts -> Local, Mutect2.MergeVCFs -> Local, Mutect2.SumSubBamouts -> Local, Mutect2.SplitIntervals -> Local, Mutect2.SumSubVcfs -> Local, Mutect2.Filter -> Local, Mutect2.oncotate_m2 -> Local [2018-10-09 00:44:22,05] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,05] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,05] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:22,06] [warn] Local [ec34099b]: Key/s [preemptible, bootDiskSizeGb, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-10-09 00:44:24,43] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Condition NOT met: 'defined(realignment_index_bundle)'. Bypassing conditional section [2018-10-09 00:44:24,44] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Condition met: 'defined(variants_for_contamination)'. Running conditional section [2018-10-09 00:44:25,46] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Condition NOT met: 'run_oncotator_or_default'. Bypassing conditional section [2018-10-09 00:44:25,46] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Condition NOT met: 'run_ob_filter && !defined(tumor_sequencing_artifact_metrics)'. Bypassing conditional section [2018-10-09 00:44:25,48] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Condition NOT met: 'run_funcotator_or_default'. Bypassing conditional section [2018-10-09 00:44:25,49] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Condition NOT met: 'run_ob_filter'. Bypassing conditional section [2018-10-09 00:44:25,49] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Condition NOT met: 'make_bamout_or_default'. Bypassing conditional section [2018-10-09 00:44:26,56] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Starting Mutect2.CalculateContamination, Mutect2.SplitIntervals [2018-10-09 00:44:28,70] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.CalculateContamination:NA:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, memory [2018-10-09 00:44:28,70] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.SplitIntervals:NA:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:29,01] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.SplitIntervals:NA:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar mkdir interval-files gatk --java-options "-Xmx3000m" SplitIntervals \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ \ -scatter 50 \ -O interval-files \ cp interval-files/*.intervals . [2018-10-09 00:44:29,01] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.CalculateContamination:NA:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx6500m" GetPileupSummaries -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/inputs/-314364064/mytestN.hg38.bam -V /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/inputs/1437983679/small_exac_common_3.hg38.vcf.gz -O normal_pileups.table NORMAL_CMD="-matched normal_pileups.table" fi gatk --java-options "-Xmx6500m" GetPileupSummaries -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/inputs/-314364064/mytestT.hg38.bam -V /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/inputs/1437983679/small_exac_common_3.hg38.vcf.gz -O pileups.table gatk --java-options "-Xmx6500m" CalculateContamination -I pileups.table -O contamination.table --tumor-segmentation segments.table $NORMAL_CMD [2018-10-09 00:44:29,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.SplitIntervals:NA:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:29,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.CalculateContamination:NA:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-CalculateContamination/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:30,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.CalculateContamination:NA:1]: job id: 10682 [2018-10-09 00:44:30,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.SplitIntervals:NA:1]: job id: 10681 [2018-10-09 00:44:30,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.SplitIntervals:NA:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:30,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.CalculateContamination:NA:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:38,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.SplitIntervals:NA:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:44:44,13] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Starting Mutect2.M2 (17 shards) [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:16:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:42:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:47:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:35:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:32:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:48:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:33:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:8:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:1:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:0:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:45:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:7:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:24:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:39:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:9:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:43:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:38:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:44,69] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/1547804351/0038-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0038-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,70] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/1547804351/0032-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0032-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,78] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/1547804351/0009-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0009-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,78] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/1547804351/0043-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0043-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,79] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/1547804351/0039-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0039-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,80] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/1547804351/0007-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0007-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,81] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/1547804351/0035-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0035-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,82] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/1547804351/0008-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0008-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,82] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/1547804351/0001-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0001-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,83] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/1547804351/0024-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0024-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,83] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/1547804351/0042-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0042-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,84] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:38:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/1547804351/0038-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:44,84] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/1547804351/0045-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0045-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,85] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/1547804351/0033-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0033-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,86] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/1547804351/0048-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0048-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,86] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/1547804351/0000-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0000-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,87] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/1547804351/0016-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0016-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,87] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:38:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:44,90] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/1547804351/0047-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0047-scattered.intervals: Operation not permitted [2018-10-09 00:44:44,91] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:32:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/1547804351/0032-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:44,96] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:39:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/1547804351/0039-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:44,96] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:9:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/1547804351/0009-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,03] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:43:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/1547804351/0043-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,04] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:32:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,04] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:7:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/1547804351/0007-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,04] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:35:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/inputs/1547804351/0035-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:9:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:39:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:8:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/inputs/1547804351/0008-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:1:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/inputs/1547804351/0001-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:42:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/1547804351/0042-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:24:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/inputs/1547804351/0024-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:45:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/inputs/1547804351/0045-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:43:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:33:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/1547804351/0033-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:16:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/1547804351/0016-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:35:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-35/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:7:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:48:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/inputs/1547804351/0048-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,07] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:24:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-24/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,07] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:0:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/inputs/1547804351/0000-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,07] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:47:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/1547804351/0047-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,11] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:42:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,13] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:1:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-1/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,21] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:8:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-8/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,21] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:33:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,21] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:45:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-45/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,21] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:16:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,21] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:48:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-48/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:0:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-0/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,23] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:47:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,23] [info] WorkflowExecutionActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 [ec34099b]: Starting Mutect2.M2 (33 shards) [2018-10-09 00:44:45,58] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:31:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:34:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:27:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:21:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,59] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:23:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:26:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:40:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:18:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:46:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:11:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:2:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:38:1]: job id: 11044 [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:9:1]: job id: 11066 [2018-10-09 00:44:45,60] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:22:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:32:1]: job id: 11053 [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:39:1]: job id: 11068 [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:43:1]: job id: 11095 [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:9:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:7:1]: job id: 11099 [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:38:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:32:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,60] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:39:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:42:1]: job id: 11124 [2018-10-09 00:44:45,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:42:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:35:1]: job id: 11104 [2018-10-09 00:44:45,61] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/1547804351/0031-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0031-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:24:1]: job id: 11111 [2018-10-09 00:44:45,61] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:29:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,61] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:49:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,61] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:3:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,61] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:20:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:24:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:43:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,62] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:7:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,62] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:6:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,62] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/1547804351/0034-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0034-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,62] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:10:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,62] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:16:1]: job id: 11169 [2018-10-09 00:44:45,62] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:45:1]: job id: 11161 [2018-10-09 00:44:45,62] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:0:1]: job id: 11230 [2018-10-09 00:44:45,62] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:35:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:28:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:45:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:48:1]: job id: 11164 [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:8:1]: job id: 11163 [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:0:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:1:1]: job id: 11128 [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:17:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:5:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:41:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:16:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:33:1]: job id: 11170 [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:47:1]: job id: 11228 [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:25:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:4:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:12:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:8:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:48:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:33:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:47:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:37:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:1:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:14:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:19:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:15:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:44:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:13:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:36:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,63] [warn] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:30:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, cpu, memory [2018-10-09 00:44:45,64] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/1547804351/0021-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0021-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,64] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/1547804351/0027-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0027-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,66] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/1547804351/0023-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0023-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,67] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/1547804351/0040-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0040-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,72] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/1547804351/0026-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0026-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,72] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/1547804351/0018-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0018-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,72] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/1547804351/0049-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0049-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,74] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:21:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/1547804351/0021-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,74] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:31:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/1547804351/0031-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,75] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/1547804351/0020-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0020-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,77] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/1547804351/0022-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0022-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,77] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/1547804351/0046-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0046-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,77] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/1547804351/0011-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0011-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,77] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:34:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/inputs/1547804351/0034-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,78] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/1547804351/0002-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0002-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,79] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/1547804351/0006-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0006-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,80] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:21:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,80] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:31:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,81] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/1547804351/0041-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0041-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,81] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/1547804351/0010-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0010-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,82] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:27:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/1547804351/0027-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,86] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/1547804351/0005-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0005-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,86] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:34:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-34/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,87] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/1547804351/0019-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0019-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,87] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/1547804351/0028-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0028-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,89] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:23:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/1547804351/0023-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,90] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:27:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,90] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:40:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/inputs/1547804351/0040-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,90] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/1547804351/0004-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0004-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,90] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/1547804351/0017-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0017-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,91] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/1547804351/0037-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0037-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,91] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:26:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/inputs/1547804351/0026-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,92] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:49:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/1547804351/0049-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,93] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:20:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/1547804351/0020-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,93] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/1547804351/0003-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0003-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,93] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:11:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/inputs/1547804351/0011-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,93] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/1547804351/0025-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0025-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,94] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:22:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/inputs/1547804351/0022-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,94] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/1547804351/0012-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0012-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,94] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/1547804351/0030-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0030-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,95] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/1547804351/0036-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0036-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,94] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/1547804351/0013-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0013-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,95] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:40:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-40/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,96] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:18:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/1547804351/0018-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,96] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:26:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-26/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,96] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:23:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,96] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/1547804351/0014-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0014-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,97] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:49:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,97] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/1547804351/0029-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0029-scattered.intervals: Operation not permitted [2018-10-09 00:44:45,97] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:2:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/1547804351/0002-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,98] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:46:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/1547804351/0046-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:45,98] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:11:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-11/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,99] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:20:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:45,99] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/1547804351/0044-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0044-scattered.intervals: Operation not permitted [2018-10-09 00:44:46,00] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:10:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/1547804351/0010-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,01] [warn] Localization via hard link has failed: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/1547804351/0015-scattered.intervals -> /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-SplitIntervals/execution/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0015-scattered.intervals: Operation not permitted [2018-10-09 00:44:46,01] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:22:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-22/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,01] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:41:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/1547804351/0041-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,02] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:18:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,02] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:2:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,09] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:6:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/1547804351/0006-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,10] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:46:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,11] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:10:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,12] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:41:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,12] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:4:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/inputs/1547804351/0004-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,13] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:5:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/1547804351/0005-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,14] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:17:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/inputs/1547804351/0017-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,14] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:6:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,14] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:19:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/1547804351/0019-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,14] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:28:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/1547804351/0028-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,17] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:25:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/1547804351/0025-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,17] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:5:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,17] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:4:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-4/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,18] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:44:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/1547804351/0044-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,18] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:13:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/1547804351/0013-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,21] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:3:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/1547804351/0003-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:17:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-17/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:28:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:12:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/1547804351/0012-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:19:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:13:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:30:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/1547804351/0030-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,22] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:37:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/1547804351/0037-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,23] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:3:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,23] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:29:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/1547804351/0029-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,23] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:25:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,24] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:12:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,24] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:36:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/inputs/1547804351/0036-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,24] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:30:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,24] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:44:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,25] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:15:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/1547804351/0015-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,25] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:14:1]: set -e export GATK_LOCAL_JAR=/root/gatk.jar # We need to create these files regardless, even if they stay empty touch bamout.bam echo "" > normal_name.txt gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode tumor_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-314364064/mytestT.hg38.bam -tumor cat tumor_name.txt" if [[ -f "/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-314364064/mytestN.hg38.bam" ]]; then gatk --java-options "-Xmx3000m" GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode normal_command_line="-I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-314364064/mytestN.hg38.bam -normal cat normal_name.txt" fi gatk --java-options "-Xmx3000m" Mutect2 \ -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/-1601801936/Homo_sapiens_assembly38.fasta \ $tumor_command_line \ $normal_command_line \ --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/1437983679/af-only-gnomad.hg38.vcf.gz \ \ -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/inputs/1547804351/0014-scattered.intervals \ \ -O "output.vcf" \ \ [2018-10-09 00:44:46,26] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:37:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,26] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:29:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,27] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:36:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-36/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,30] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:15:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:46,30] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:14:1]: executing: # make sure there is no preexisting Docker CID file rm -f /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/execution/docker_cid # run as in the original configuration without --rm flag (will remove later) docker run \ --cidfile /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/execution/docker_cid \ -i \ \ --entrypoint /bin/bash \ -v /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14:/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14 \ broadinstitute/gatk@sha256:971cc33076d1a6cc09b8b93368bdecd5ac02fffb7d5c9adb949c4b22cd73be89 /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/execution/script # get the return code (working even if the container was detached) rc=$(docker wait cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/execution/docker_cid) # remove the container after waiting docker rm cat /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-14/execution/docker_cid # return exit code exit $rc [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:31:1]: job id: 12306 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:21:1]: job id: 12305 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:26:1]: job id: 12552 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:27:1]: job id: 12348 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:34:1]: job id: 12346 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:23:1]: job id: 12543 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:11:1]: job id: 12580 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:49:1]: job id: 12554 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:20:1]: job id: 12581 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:2:1]: job id: 12639 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:18:1]: job id: 12628 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:10:1]: job id: 12657 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:28:1]: job id: 12863 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:6:1]: job id: 12790 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:22:1]: job id: 12617 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:3:1]: job id: 12929 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:17:1]: job id: 12867 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:19:1]: job id: 12891 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:41:1]: job id: 12716 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:30:1]: job id: 12938 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:13:1]: job id: 12889 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:4:1]: job id: 12823 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:15:1]: job id: 13107 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:37:1]: job id: 13022 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:44:1]: job id: 12942 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:5:1]: job id: 12841 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:29:1]: job id: 13049 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:25:1]: job id: 12950 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:12:1]: job id: 12948 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:46:1]: job id: 12638 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:36:1]: job id: 13103 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:14:1]: job id: 13110 [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:27:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:2:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:6:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:22:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:10:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:19:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:3:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:30:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:4:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:17:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:41:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:15:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:13:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:37:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:44:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:12:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:29:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:20:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:25:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:36:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:21:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:46:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:14:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:26:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:23:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:40:1]: job id: 12542 [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:28:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:18:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:5:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:31:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:49:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:34:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:40:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:44:50,65] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:11:1]: Status change from - to WaitingForReturnCodeFile [2018-10-09 00:46:45,52] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:6:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:46:49,83] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:19:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:47:18,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:28:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:47:32,97] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:25:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:47:39,44] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:47:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:47:54,00] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:43:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:47:55,67] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.CalculateContamination:NA:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:15,61] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:49:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:22,82] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:7:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:36,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:16:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:36,21] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:37:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:45,64] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:18:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:45,70] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:3:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:53,27] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:41:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:58,90] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:32:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:48:59,34] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:10:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:49:01,23] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:2:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:49:09,25] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:21:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:49:26,05] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:42:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:49:54,00] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:12:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:49:55,23] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:30:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:50:04,56] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:9:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:50:07,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:46:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:50:31,99] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:23:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:50:56,36] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:13:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:51:37,63] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:34:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:51:47,95] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:38:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:52:02,82] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:24:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:52:37,88] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:33:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:52:38,43] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:35:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:53:05,97] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:48:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:53:35,25] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:27:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:53:45,66] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:29:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:54:09,47] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:31:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:54:21,31] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:17:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:54:46,30] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:15:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:55:37,91] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:45:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:56:33,24] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:40:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:56:41,50] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:5:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:57:03,36] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:11:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:57:06,66] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:14:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:57:50,07] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:1:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:58:09,01] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:22:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:58:09,89] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:44:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:58:32,67] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:0:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:58:41,01] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:36:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:58:49,89] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:8:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:59:24,03] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:4:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:59:25,58] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:20:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 00:59:33,06] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:26:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 01:01:13,75] [info] BackgroundConfigAsyncJobExecutionActor [ec34099bMutect2.M2:39:1]: Status change from WaitingForReturnCodeFile to Done [2018-10-09 01:01:14,78] [error] WorkflowManagerActor Workflow ec34099b-7f45-4a33-b205-0cd6011f53f0 failed (during ExecutingWorkflowState): Job Mutect2.M2:46:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/tmp.83420e2f 16:45:04.351 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:05.081 INFO GetSampleName - ------------------------------------------------------------ 16:45:05.081 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:05.083 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:05.084 INFO GetSampleName - Executing as root@a9c8babafa73 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:05.085 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:05.085 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:04 PM UTC 16:45:05.085 INFO GetSampleName - ------------------------------------------------------------ 16:45:05.085 INFO GetSampleName - ------------------------------------------------------------ 16:45:05.086 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:05.086 INFO GetSampleName - Picard Version: 2.18.7 16:45:05.086 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:05.086 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:05.091 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:05.091 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:05.091 INFO GetSampleName - Deflater: IntelDeflater 16:45:05.091 INFO GetSampleName - Inflater: IntelInflater 16:45:05.092 INFO GetSampleName - GCS max retries/reopens: 20 16:45:05.092 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:05.129 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:05.129 INFO GetSampleName - Initializing engine 16:45:10.800 INFO GetSampleName - Done initializing engine 16:45:10.861 INFO ProgressMeter - Starting traversal 16:45:10.862 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:10.863 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:10.863 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:10.863 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:10 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1736441856 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/tmp.83420e2f 16:45:28.793 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:29.724 INFO GetSampleName - ------------------------------------------------------------ 16:45:29.724 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:29.724 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:29.725 INFO GetSampleName - Executing as root@a9c8babafa73 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:29.725 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:29.725 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:28 PM UTC 16:45:29.725 INFO GetSampleName - ------------------------------------------------------------ 16:45:29.725 INFO GetSampleName - ------------------------------------------------------------ 16:45:29.726 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:29.726 INFO GetSampleName - Picard Version: 2.18.7 16:45:29.726 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:29.726 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:29.726 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:29.726 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:29.726 INFO GetSampleName - Deflater: IntelDeflater 16:45:29.726 INFO GetSampleName - Inflater: IntelInflater 16:45:29.751 INFO GetSampleName - GCS max retries/reopens: 20 16:45:29.751 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:29.751 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:29.751 INFO GetSampleName - Initializing engine 16:45:35.516 INFO GetSampleName - Done initializing engine 16:45:35.575 INFO ProgressMeter - Starting traversal 16:45:35.575 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:35.577 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:35.577 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:35.577 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:35 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1758461952 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/tmp.83420e2f 16:45:55.375 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:56.371 INFO Mutect2 - ------------------------------------------------------------ 16:45:56.371 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:56.372 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:56.379 INFO Mutect2 - Executing as root@a9c8babafa73 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:56.379 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:56.380 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:55 PM UTC 16:45:56.380 INFO Mutect2 - ------------------------------------------------------------ 16:45:56.380 INFO Mutect2 - ------------------------------------------------------------ 16:45:56.393 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:56.393 INFO Mutect2 - Picard Version: 2.18.7 16:45:56.393 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:56.394 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:56.394 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:56.394 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:56.394 INFO Mutect2 - Deflater: IntelDeflater 16:45:56.394 INFO Mutect2 - Inflater: IntelInflater 16:45:56.394 INFO Mutect2 - GCS max retries/reopens: 20 16:45:56.394 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:56.394 INFO Mutect2 - Initializing engine 16:46:03.653 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:06.055 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:06.320 INFO Mutect2 - Done initializing engine 16:46:06.727 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:06.744 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:06.903 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:06.904 INFO IntelPairHmm - Available threads: 24 16:46:06.904 INFO IntelPairHmm - Requested threads: 4 16:46:06.904 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:08.172 INFO ProgressMeter - Starting traversal 16:46:08.172 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:18.401 INFO ProgressMeter - chrX:85110200 0.2 520 3050.7 16:46:28.448 INFO ProgressMeter - chrX:85700383 0.3 2530 7487.1 16:46:38.810 INFO ProgressMeter - chrX:86128701 0.5 3990 7813.8 16:46:48.868 INFO ProgressMeter - chrX:86195919 0.7 4220 6221.9 16:46:58.900 INFO ProgressMeter - chrX:86536588 0.8 5380 6363.3 16:47:09.293 INFO ProgressMeter - chrX:87084544 1.0 7240 7107.2 16:47:19.333 INFO ProgressMeter - chrX:87657532 1.2 9190 7753.0 16:47:29.311 INFO ProgressMeter - chrX:89748569 1.4 16260 12023.8 16:47:39.314 INFO ProgressMeter - chrX:94256895 1.5 31490 20730.3 16:47:49.319 INFO ProgressMeter - chrX:96623977 1.7 39530 23449.0 16:47:59.324 INFO ProgressMeter - chrX:99108959 1.9 47970 25894.5 16:48:12.774 INFO ProgressMeter - chrX:100804373 2.1 53770 25892.0 16:48:29.122 INFO ProgressMeter - chrX:101358398 2.3 55680 23702.2 16:48:39.121 INFO ProgressMeter - chrX:105381543 2.5 69320 27553.7 16:48:49.128 INFO ProgressMeter - chrX:109882918 2.7 84660 31558.9 16:49:00.269 INFO ProgressMeter - chrX:113779558 2.9 97920 34138.9 16:49:10.272 INFO ProgressMeter - chrX:120581291 3.0 121040 39881.4 16:49:21.411 INFO ProgressMeter - chrX:124053113 3.2 132850 41249.4 16:49:24.655 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.098259223 16:49:24.655 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 32.710448672000005 16:49:24.655 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 14.06 sec 16:49:24.656 INFO Mutect2 - Shutting down engine [October 8, 2018 4:49:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 3.49 minutes. Runtime.totalMemory()=2169503744 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chrX start:224664443 stop:224664487 contigLength:156040895 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-46/inputs/1547804351/0046-scattered.intervals -O output.vcf Job Mutect2.M2:33:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/tmp.73126278 16:44:58.551 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:44:59.481 INFO GetSampleName - ------------------------------------------------------------ 16:44:59.481 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:44:59.481 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:44:59.482 INFO GetSampleName - Executing as root@ee6dbb0373ae on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:44:59.486 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:44:59.486 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:58 PM UTC 16:44:59.486 INFO GetSampleName - ------------------------------------------------------------ 16:44:59.486 INFO GetSampleName - ------------------------------------------------------------ 16:44:59.487 INFO GetSampleName - HTSJDK Version: 2.16.0 16:44:59.487 INFO GetSampleName - Picard Version: 2.18.7 16:44:59.487 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:44:59.487 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:44:59.488 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:44:59.488 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:44:59.488 INFO GetSampleName - Deflater: IntelDeflater 16:44:59.488 INFO GetSampleName - Inflater: IntelInflater 16:44:59.488 INFO GetSampleName - GCS max retries/reopens: 20 16:44:59.488 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:44:59.490 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:44:59.490 INFO GetSampleName - Initializing engine 16:45:05.349 INFO GetSampleName - Done initializing engine 16:45:05.402 INFO ProgressMeter - Starting traversal 16:45:05.402 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:05.403 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:05.404 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:05.404 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:05 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1729101824 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/tmp.73126278 16:45:23.065 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:23.977 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.977 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:23.977 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:23.978 INFO GetSampleName - Executing as root@ee6dbb0373ae on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:23.978 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:23.978 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:22 PM UTC 16:45:23.978 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.978 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.979 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:23.979 INFO GetSampleName - Picard Version: 2.18.7 16:45:23.979 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:23.979 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:23.979 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:23.979 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:23.980 INFO GetSampleName - Deflater: IntelDeflater 16:45:23.980 INFO GetSampleName - Inflater: IntelInflater 16:45:23.980 INFO GetSampleName - GCS max retries/reopens: 20 16:45:23.980 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:23.980 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:23.980 INFO GetSampleName - Initializing engine 16:45:29.591 INFO GetSampleName - Done initializing engine 16:45:29.650 INFO ProgressMeter - Starting traversal 16:45:29.651 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:29.652 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:29.652 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:29.652 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:29 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1794637824 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/tmp.73126278 16:45:48.368 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:49.429 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.430 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:49.430 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:49.430 INFO Mutect2 - Executing as root@ee6dbb0373ae on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:49.430 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:49.430 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:48 PM UTC 16:45:49.431 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.431 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.431 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:49.431 INFO Mutect2 - Picard Version: 2.18.7 16:45:49.431 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:49.431 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:49.431 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:49.431 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:49.433 INFO Mutect2 - Deflater: IntelDeflater 16:45:49.433 INFO Mutect2 - Inflater: IntelInflater 16:45:49.433 INFO Mutect2 - GCS max retries/reopens: 20 16:45:49.433 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:49.433 INFO Mutect2 - Initializing engine 16:45:56.214 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:58.386 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:58.737 INFO Mutect2 - Done initializing engine 16:45:59.935 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:00.027 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:00.220 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:00.221 INFO IntelPairHmm - Available threads: 24 16:46:00.221 INFO IntelPairHmm - Requested threads: 4 16:46:00.221 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:01.698 INFO ProgressMeter - Starting traversal 16:46:01.698 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:11.766 INFO ProgressMeter - chr13:46527050 0.2 420 2503.5 16:46:22.060 INFO ProgressMeter - chr13:46864052 0.3 1590 4695.6 16:46:32.071 INFO ProgressMeter - chr13:47077436 0.5 2330 4602.9 16:46:42.371 INFO ProgressMeter - chr13:47343571 0.7 3260 4809.2 16:46:52.446 INFO ProgressMeter - chr13:47551331 0.8 3990 4717.5 16:47:02.644 INFO ProgressMeter - chr13:47739257 1.0 4660 4587.7 16:47:12.764 INFO ProgressMeter - chr13:48094932 1.2 5920 4998.3 16:47:33.534 INFO ProgressMeter - chr13:48308014 1.5 6670 4357.8 16:47:46.473 INFO ProgressMeter - chr13:48348806 1.7 6820 3905.5 16:47:56.584 INFO ProgressMeter - chr13:48362949 1.9 6880 3593.2 16:48:11.216 INFO ProgressMeter - chr13:48374783 2.2 6930 3210.4 16:48:42.966 INFO ProgressMeter - chr13:48381323 2.7 6960 2589.5 16:48:53.351 INFO ProgressMeter - chr13:48452902 2.9 7210 2520.2 16:49:03.958 INFO ProgressMeter - chr13:48459835 3.0 7240 2383.4 16:49:20.893 INFO ProgressMeter - chr13:48467516 3.3 7270 2189.8 16:49:30.905 INFO ProgressMeter - chr13:50536507 3.5 14540 4170.1 16:49:40.915 INFO ProgressMeter - chr13:52071758 3.7 19930 5454.9 16:49:50.964 INFO ProgressMeter - chr13:55194798 3.8 30720 8039.6 16:50:00.964 INFO ProgressMeter - chr13:58852226 4.0 43380 10878.3 16:50:10.973 INFO ProgressMeter - chr13:63466961 4.2 59310 14275.9 16:50:20.992 INFO ProgressMeter - chr13:66883103 4.3 71120 16457.1 16:50:30.993 INFO ProgressMeter - chr13:68489929 4.5 76650 17078.0 16:50:41.100 INFO ProgressMeter - chr13:71705010 4.7 87730 18839.6 16:50:51.862 INFO ProgressMeter - chr13:72705426 4.8 91190 18856.3 16:51:01.865 INFO ProgressMeter - chr13:75950821 5.0 102530 20494.7 16:51:13.046 INFO ProgressMeter - chr13:78761630 5.2 112270 21635.7 16:51:23.052 INFO ProgressMeter - chr13:83663798 5.4 129290 24139.8 16:51:33.072 INFO ProgressMeter - chr13:88901729 5.5 147360 26681.7 16:51:43.083 INFO ProgressMeter - chr13:93831147 5.7 164420 28897.7 16:51:49.396 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.227691937 16:51:49.397 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 124.041635416 16:51:49.397 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 32.78 sec 16:51:49.398 INFO Mutect2 - Shutting down engine [October 8, 2018 4:51:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 6.02 minutes. Runtime.totalMemory()=2107113472 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr13 start:144834452 stop:144834541 contigLength:114364328 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-33/inputs/1547804351/0033-scattered.intervals -O output.vcf Job Mutect2.M2:27:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/tmp.37165e06 16:45:02.713 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:04.091 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.091 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:04.093 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:04.100 INFO GetSampleName - Executing as root@8519b104d899 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:04.100 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:04.100 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:02 PM UTC 16:45:04.100 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.101 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.101 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:04.101 INFO GetSampleName - Picard Version: 2.18.7 16:45:04.101 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:04.101 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:04.118 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:04.118 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:04.118 INFO GetSampleName - Deflater: IntelDeflater 16:45:04.118 INFO GetSampleName - Inflater: IntelInflater 16:45:04.118 INFO GetSampleName - GCS max retries/reopens: 20 16:45:04.119 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:04.120 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:04.120 INFO GetSampleName - Initializing engine 16:45:09.742 INFO GetSampleName - Done initializing engine 16:45:09.804 INFO ProgressMeter - Starting traversal 16:45:09.804 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:09.805 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:09.806 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:09.806 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:09 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1742209024 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/tmp.37165e06 16:45:27.970 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:29.993 INFO GetSampleName - ------------------------------------------------------------ 16:45:29.993 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:29.993 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:30.000 INFO GetSampleName - Executing as root@8519b104d899 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:30.001 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:30.001 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:27 PM UTC 16:45:30.001 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.001 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.021 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:30.021 INFO GetSampleName - Picard Version: 2.18.7 16:45:30.021 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:30.021 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:30.022 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:30.022 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:30.022 INFO GetSampleName - Deflater: IntelDeflater 16:45:30.022 INFO GetSampleName - Inflater: IntelInflater 16:45:30.022 INFO GetSampleName - GCS max retries/reopens: 20 16:45:30.022 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:30.022 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:30.022 INFO GetSampleName - Initializing engine 16:45:36.099 INFO GetSampleName - Done initializing engine 16:45:36.146 INFO ProgressMeter - Starting traversal 16:45:36.147 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:36.148 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:36.148 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:36.149 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:36 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=1811415040 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/tmp.37165e06 16:45:53.495 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:54.756 INFO Mutect2 - ------------------------------------------------------------ 16:45:54.756 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:54.795 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:54.796 INFO Mutect2 - Executing as root@8519b104d899 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:54.796 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:54.796 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:53 PM UTC 16:45:54.796 INFO Mutect2 - ------------------------------------------------------------ 16:45:54.796 INFO Mutect2 - ------------------------------------------------------------ 16:45:54.797 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:54.797 INFO Mutect2 - Picard Version: 2.18.7 16:45:54.797 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:54.797 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:54.797 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:54.797 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:54.797 INFO Mutect2 - Deflater: IntelDeflater 16:45:54.797 INFO Mutect2 - Inflater: IntelInflater 16:45:54.797 INFO Mutect2 - GCS max retries/reopens: 20 16:45:54.797 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:54.797 INFO Mutect2 - Initializing engine 16:46:01.686 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:03.832 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:04.122 INFO Mutect2 - Done initializing engine 16:46:04.498 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:04.594 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:04.877 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:04.879 INFO IntelPairHmm - Available threads: 24 16:46:04.879 INFO IntelPairHmm - Requested threads: 4 16:46:04.880 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:06.341 INFO ProgressMeter - Starting traversal 16:46:06.341 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:16.361 INFO ProgressMeter - chr10:62576044 0.2 320 1916.4 16:46:26.387 INFO ProgressMeter - chr10:62776889 0.3 1020 3053.0 16:46:36.507 INFO ProgressMeter - chr10:62958276 0.5 1660 3301.7 16:46:47.189 INFO ProgressMeter - chr10:63143498 0.7 2320 3407.8 16:46:57.257 INFO ProgressMeter - chr10:63344982 0.8 3030 3570.7 16:47:07.346 INFO ProgressMeter - chr10:63651871 1.0 4110 4042.3 16:47:17.355 INFO ProgressMeter - chr10:64109136 1.2 5710 4824.5 16:47:27.538 INFO ProgressMeter - chr10:64667327 1.4 7660 5660.3 16:47:37.539 INFO ProgressMeter - chr10:66409550 1.5 13760 9052.9 16:48:08.182 INFO ProgressMeter - chr10:67795142 2.0 18590 9154.6 16:48:18.559 INFO ProgressMeter - chr10:68175804 2.2 19950 9053.2 16:48:37.487 INFO ProgressMeter - chr10:69779427 2.5 25690 10198.1 16:48:56.702 INFO ProgressMeter - chr10:70164394 2.8 27070 9533.9 16:49:06.708 INFO ProgressMeter - chr10:72366387 3.0 34950 11626.3 16:49:29.176 INFO ProgressMeter - chr10:72918702 3.4 36920 10921.2 16:49:55.578 INFO ProgressMeter - chr10:73201460 3.8 37940 9930.3 16:50:05.578 INFO ProgressMeter - chr10:75245006 4.0 45220 11341.1 16:50:15.583 INFO ProgressMeter - chr10:78519079 4.2 56770 13666.2 16:50:28.184 INFO ProgressMeter - chr10:80128146 4.4 62510 14323.9 16:50:38.184 INFO ProgressMeter - chr10:83188678 4.5 73290 16176.2 16:50:48.196 INFO ProgressMeter - chr10:87058023 4.7 86900 18498.9 16:50:58.514 INFO ProgressMeter - chr10:87866198 4.9 89720 18424.7 16:51:08.580 INFO ProgressMeter - chr10:87896610 5.0 89830 17832.9 16:51:43.487 INFO ProgressMeter - chr10:87925995 5.6 89940 16006.1 16:51:57.901 INFO ProgressMeter - chr10:87934486 5.9 89980 15356.7 16:52:11.413 INFO ProgressMeter - chr10:87959032 6.1 90080 14804.8 16:52:21.534 INFO ProgressMeter - chr10:87961060 6.3 90090 14407.0 16:52:31.553 INFO ProgressMeter - chr10:91871132 6.4 103780 16164.6 16:52:33.315 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.13996529300000002 16:52:33.315 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 164.869361117 16:52:33.315 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 37.80 sec 16:52:33.316 INFO Mutect2 - Shutting down engine [October 8, 2018 4:52:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 6.67 minutes. Runtime.totalMemory()=2081947648 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr10 start:141995990 stop:141996080 contigLength:133797422 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-27/inputs/1547804351/0027-scattered.intervals -O output.vcf Job Mutect2.M2:31:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/tmp.edb1ee7b 16:45:00.111 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:00.900 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.900 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:00.901 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:00.901 INFO GetSampleName - Executing as root@9a276203de24 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:00.901 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:00.901 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:59 PM UTC 16:45:00.901 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.901 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.905 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:00.905 INFO GetSampleName - Picard Version: 2.18.7 16:45:00.905 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:00.905 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:00.906 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:00.906 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:00.906 INFO GetSampleName - Deflater: IntelDeflater 16:45:00.906 INFO GetSampleName - Inflater: IntelInflater 16:45:00.906 INFO GetSampleName - GCS max retries/reopens: 20 16:45:00.906 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:00.906 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:00.906 INFO GetSampleName - Initializing engine 16:45:06.832 INFO GetSampleName - Done initializing engine 16:45:06.887 INFO ProgressMeter - Starting traversal 16:45:06.888 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:06.889 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:06.889 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:06.889 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:06 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1697120256 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/tmp.edb1ee7b 16:45:23.937 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:24.826 INFO GetSampleName - ------------------------------------------------------------ 16:45:24.826 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:24.826 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:24.826 INFO GetSampleName - Executing as root@9a276203de24 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:24.827 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:24.827 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:23 PM UTC 16:45:24.827 INFO GetSampleName - ------------------------------------------------------------ 16:45:24.827 INFO GetSampleName - ------------------------------------------------------------ 16:45:24.827 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:24.842 INFO GetSampleName - Picard Version: 2.18.7 16:45:24.843 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:24.843 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:24.843 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:24.843 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:24.843 INFO GetSampleName - Deflater: IntelDeflater 16:45:24.843 INFO GetSampleName - Inflater: IntelInflater 16:45:24.843 INFO GetSampleName - GCS max retries/reopens: 20 16:45:24.843 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:24.843 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:24.843 INFO GetSampleName - Initializing engine 16:45:31.758 INFO GetSampleName - Done initializing engine 16:45:31.825 INFO ProgressMeter - Starting traversal 16:45:31.826 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:31.827 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:31.827 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:31.827 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:31 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1850736640 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/tmp.edb1ee7b 16:45:49.705 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:50.799 INFO Mutect2 - ------------------------------------------------------------ 16:45:50.799 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:50.799 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:50.799 INFO Mutect2 - Executing as root@9a276203de24 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:50.799 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:50.814 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:49 PM UTC 16:45:50.814 INFO Mutect2 - ------------------------------------------------------------ 16:45:50.814 INFO Mutect2 - ------------------------------------------------------------ 16:45:50.814 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:50.814 INFO Mutect2 - Picard Version: 2.18.7 16:45:50.815 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:50.815 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:50.815 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:50.815 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:50.815 INFO Mutect2 - Deflater: IntelDeflater 16:45:50.815 INFO Mutect2 - Inflater: IntelInflater 16:45:50.815 INFO Mutect2 - GCS max retries/reopens: 20 16:45:50.815 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:50.815 INFO Mutect2 - Initializing engine 16:45:56.880 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:58.871 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:59.259 INFO Mutect2 - Done initializing engine 16:45:59.950 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:00.032 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:00.188 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:00.188 INFO IntelPairHmm - Available threads: 24 16:46:00.188 INFO IntelPairHmm - Requested threads: 4 16:46:00.188 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:01.482 INFO ProgressMeter - Starting traversal 16:46:01.482 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:11.579 INFO ProgressMeter - chr12:51035395 0.2 170 1017.7 16:46:21.623 INFO ProgressMeter - chr12:51307814 0.3 1130 3366.3 16:46:31.671 INFO ProgressMeter - chr12:51506487 0.5 1830 3637.2 16:46:41.926 INFO ProgressMeter - chr12:51819070 0.7 2910 4317.1 16:46:53.438 INFO ProgressMeter - chr12:51977159 0.9 3480 4018.8 16:47:34.691 INFO ProgressMeter - chr12:51982393 1.6 3500 2253.0 16:47:48.627 INFO ProgressMeter - chr12:51984139 1.8 3510 1965.6 16:48:30.489 INFO ProgressMeter - chr12:51989035 2.5 3530 1421.4 16:48:40.491 INFO ProgressMeter - chr12:53092312 2.7 7440 2807.4 16:48:50.513 INFO ProgressMeter - chr12:54427515 2.8 12180 4323.5 16:49:00.534 INFO ProgressMeter - chr12:56532055 3.0 19540 6547.9 16:49:13.099 INFO ProgressMeter - chr12:57751662 3.2 23910 7486.8 16:49:23.108 INFO ProgressMeter - chr12:59703469 3.4 30680 9129.8 16:49:34.765 INFO ProgressMeter - chr12:61775878 3.6 37880 10656.3 16:49:44.765 INFO ProgressMeter - chr12:64911847 3.7 48820 13118.8 16:49:59.011 INFO ProgressMeter - chr12:66039295 4.0 52760 13327.2 16:50:20.656 INFO ProgressMeter - chr12:68810189 4.3 62410 14448.2 16:50:32.117 INFO ProgressMeter - chr12:68828802 4.5 62490 13854.1 16:50:52.807 INFO ProgressMeter - chr12:68840262 4.9 62540 12880.5 16:51:02.813 INFO ProgressMeter - chr12:73675659 5.0 79300 15789.9 16:51:16.645 INFO ProgressMeter - chr12:76662270 5.3 89680 17073.1 16:51:30.627 INFO ProgressMeter - chr12:77942374 5.5 94170 17166.3 16:51:40.786 INFO ProgressMeter - chr12:77995335 5.7 94370 16687.7 16:51:53.489 INFO ProgressMeter - chr12:78007069 5.9 94420 16094.0 16:52:04.137 INFO ProgressMeter - chr12:78117657 6.0 94820 15687.6 16:52:15.134 INFO ProgressMeter - chr12:78127838 6.2 94870 15234.0 16:52:25.157 INFO ProgressMeter - chr12:78159441 6.4 94990 14854.8 16:52:43.724 INFO ProgressMeter - chr12:78177372 6.7 95060 14179.6 16:52:56.708 INFO ProgressMeter - chr12:78199745 6.9 95160 13750.6 16:53:06.729 INFO ProgressMeter - chr12:80325761 7.1 102540 14467.8 16:53:16.750 INFO ProgressMeter - chr12:86150657 7.3 122710 16915.1 16:53:24.937 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.260403275 16:53:24.937 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 219.16701161100002 16:53:24.937 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 49.01 sec 16:53:24.954 INFO Mutect2 - Shutting down engine [October 8, 2018 4:53:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 7.59 minutes. Runtime.totalMemory()=2187853824 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr12 start:180538108 stop:180538215 contigLength:133275309 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-31/inputs/1547804351/0031-scattered.intervals -O output.vcf Job Mutect2.M2:42:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/tmp.8028bc10 16:44:58.502 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:00.180 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.180 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:00.180 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:00.181 INFO GetSampleName - Executing as root@9de857f3ab51 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:00.181 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:00.181 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:58 PM UTC 16:45:00.181 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.181 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.182 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:00.182 INFO GetSampleName - Picard Version: 2.18.7 16:45:00.182 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:00.182 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:00.182 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:00.182 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:00.182 INFO GetSampleName - Deflater: IntelDeflater 16:45:00.182 INFO GetSampleName - Inflater: IntelInflater 16:45:00.182 INFO GetSampleName - GCS max retries/reopens: 20 16:45:00.182 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:00.201 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:00.201 INFO GetSampleName - Initializing engine 16:45:06.351 INFO GetSampleName - Done initializing engine 16:45:06.399 INFO ProgressMeter - Starting traversal 16:45:06.400 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:06.402 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:06.402 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:06.402 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:06 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1766326272 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/tmp.8028bc10 16:45:24.361 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:25.323 INFO GetSampleName - ------------------------------------------------------------ 16:45:25.323 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:25.323 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:25.325 INFO GetSampleName - Executing as root@9de857f3ab51 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:25.325 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:25.325 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:24 PM UTC 16:45:25.325 INFO GetSampleName - ------------------------------------------------------------ 16:45:25.325 INFO GetSampleName - ------------------------------------------------------------ 16:45:25.327 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:25.327 INFO GetSampleName - Picard Version: 2.18.7 16:45:25.327 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:25.327 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:25.327 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:25.327 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:25.327 INFO GetSampleName - Deflater: IntelDeflater 16:45:25.328 INFO GetSampleName - Inflater: IntelInflater 16:45:25.328 INFO GetSampleName - GCS max retries/reopens: 20 16:45:25.328 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:25.346 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:25.346 INFO GetSampleName - Initializing engine 16:45:31.287 INFO GetSampleName - Done initializing engine 16:45:31.338 INFO ProgressMeter - Starting traversal 16:45:31.338 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:31.339 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:31.340 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:31.340 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:31 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1755316224 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/tmp.8028bc10 16:45:50.098 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:51.494 INFO Mutect2 - ------------------------------------------------------------ 16:45:51.494 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:51.510 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:51.524 INFO Mutect2 - Executing as root@9de857f3ab51 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:51.524 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:51.525 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:49 PM UTC 16:45:51.525 INFO Mutect2 - ------------------------------------------------------------ 16:45:51.525 INFO Mutect2 - ------------------------------------------------------------ 16:45:51.526 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:51.526 INFO Mutect2 - Picard Version: 2.18.7 16:45:51.526 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:51.526 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:51.526 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:51.526 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:51.527 INFO Mutect2 - Deflater: IntelDeflater 16:45:51.527 INFO Mutect2 - Inflater: IntelInflater 16:45:51.527 INFO Mutect2 - GCS max retries/reopens: 20 16:45:51.527 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:51.527 INFO Mutect2 - Initializing engine 16:45:57.993 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:00.333 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:00.572 INFO Mutect2 - Done initializing engine 16:46:00.966 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:00.984 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:01.139 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:01.140 INFO IntelPairHmm - Available threads: 24 16:46:01.140 INFO IntelPairHmm - Requested threads: 4 16:46:01.140 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:02.205 INFO ProgressMeter - Starting traversal 16:46:02.217 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:12.241 INFO ProgressMeter - chr19:48268058 0.2 380 2277.9 16:46:22.239 INFO ProgressMeter - chr19:48441643 0.3 1010 3026.8 16:46:32.330 INFO ProgressMeter - chr19:48585482 0.5 1540 3073.6 16:46:42.563 INFO ProgressMeter - chr19:48731338 0.7 2070 3078.4 16:46:52.718 INFO ProgressMeter - chr19:48946927 0.8 2850 3386.1 16:47:02.900 INFO ProgressMeter - chr19:49210621 1.0 3810 3767.1 16:47:12.900 INFO ProgressMeter - chr19:49706257 1.2 5630 4779.1 16:47:22.993 INFO ProgressMeter - chr19:50826605 1.3 9690 7197.7 16:47:32.995 INFO ProgressMeter - chr19:51885495 1.5 13440 8883.2 16:47:53.491 INFO ProgressMeter - chr19:52204211 1.9 14560 7850.9 16:48:14.830 INFO ProgressMeter - chr19:52227561 2.2 14660 6632.8 16:48:24.958 INFO ProgressMeter - chr19:53923883 2.4 20640 8675.9 16:48:29.139 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.048192926000000004 16:48:29.139 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 27.703707692000002 16:48:29.139 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 11.33 sec 16:48:29.141 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.66 minutes. Runtime.totalMemory()=2002780160 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr19 start:91043876 stop:91043954 contigLength:58617616 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-42/inputs/1547804351/0042-scattered.intervals -O output.vcf Job Mutect2.M2:38:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/tmp.0651f48a 16:44:56.015 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:44:57.563 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.564 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:44:57.564 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:44:57.564 INFO GetSampleName - Executing as root@abc9c29ae002 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:44:57.564 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:44:57.564 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:55 PM UTC 16:44:57.564 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.565 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.593 INFO GetSampleName - HTSJDK Version: 2.16.0 16:44:57.593 INFO GetSampleName - Picard Version: 2.18.7 16:44:57.594 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:44:57.594 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:44:57.594 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:44:57.594 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:44:57.594 INFO GetSampleName - Deflater: IntelDeflater 16:44:57.594 INFO GetSampleName - Inflater: IntelInflater 16:44:57.594 INFO GetSampleName - GCS max retries/reopens: 20 16:44:57.594 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:44:57.594 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:44:57.595 INFO GetSampleName - Initializing engine 16:45:03.882 INFO GetSampleName - Done initializing engine 16:45:03.922 INFO ProgressMeter - Starting traversal 16:45:03.923 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:03.924 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:03.924 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:03.924 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:03 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=1802502144 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/tmp.0651f48a 16:45:21.420 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:22.582 INFO GetSampleName - ------------------------------------------------------------ 16:45:22.582 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:22.583 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:22.583 INFO GetSampleName - Executing as root@abc9c29ae002 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:22.583 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:22.583 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:21 PM UTC 16:45:22.583 INFO GetSampleName - ------------------------------------------------------------ 16:45:22.583 INFO GetSampleName - ------------------------------------------------------------ 16:45:22.598 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:22.598 INFO GetSampleName - Picard Version: 2.18.7 16:45:22.598 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:22.599 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:22.599 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:22.599 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:22.599 INFO GetSampleName - Deflater: IntelDeflater 16:45:22.599 INFO GetSampleName - Inflater: IntelInflater 16:45:22.599 INFO GetSampleName - GCS max retries/reopens: 20 16:45:22.599 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:22.599 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:22.599 INFO GetSampleName - Initializing engine 16:45:29.304 INFO GetSampleName - Done initializing engine 16:45:29.362 INFO ProgressMeter - Starting traversal 16:45:29.363 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:29.365 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:29.365 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:29.365 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:29 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=1809842176 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/tmp.0651f48a 16:45:47.568 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:48.779 INFO Mutect2 - ------------------------------------------------------------ 16:45:48.779 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:48.795 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:48.796 INFO Mutect2 - Executing as root@abc9c29ae002 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:48.796 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:48.797 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:47 PM UTC 16:45:48.797 INFO Mutect2 - ------------------------------------------------------------ 16:45:48.797 INFO Mutect2 - ------------------------------------------------------------ 16:45:48.797 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:48.798 INFO Mutect2 - Picard Version: 2.18.7 16:45:48.803 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:48.803 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:48.803 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:48.803 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:48.803 INFO Mutect2 - Deflater: IntelDeflater 16:45:48.803 INFO Mutect2 - Inflater: IntelInflater 16:45:48.804 INFO Mutect2 - GCS max retries/reopens: 20 16:45:48.804 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:48.804 INFO Mutect2 - Initializing engine 16:45:55.412 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:57.569 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:57.879 INFO Mutect2 - Done initializing engine 16:45:58.185 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:45:58.212 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:45:58.388 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:45:58.389 INFO IntelPairHmm - Available threads: 24 16:45:58.389 INFO IntelPairHmm - Requested threads: 4 16:45:58.389 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:45:59.531 INFO ProgressMeter - Starting traversal 16:45:59.531 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:13.822 INFO ProgressMeter - chr16:46386315 0.2 5490 23052.7 16:46:24.220 INFO ProgressMeter - chr16:46387487 0.4 5500 13366.3 16:46:45.298 INFO ProgressMeter - chr16:46389283 0.8 5510 7223.7 16:47:02.876 INFO ProgressMeter - chr16:46390899 1.1 5520 5228.5 16:47:24.460 INFO ProgressMeter - chr16:46395887 1.4 5550 3921.0 16:47:45.297 INFO ProgressMeter - chr16:46399755 1.8 5570 3159.8 16:47:55.311 INFO ProgressMeter - chr16:46671697 1.9 6520 3378.8 16:48:15.161 INFO ProgressMeter - chr16:46791825 2.3 6950 3074.5 16:48:25.232 INFO ProgressMeter - chr16:48654781 2.4 13410 5522.3 16:48:45.834 INFO ProgressMeter - chr16:50751556 2.8 20740 7482.8 16:49:05.845 INFO ProgressMeter - chr16:50781345 3.1 20860 6717.7 16:49:15.902 INFO ProgressMeter - chr16:51152472 3.3 22170 6773.9 16:49:25.965 INFO ProgressMeter - chr16:52269958 3.4 26020 7562.7 16:49:35.969 INFO ProgressMeter - chr16:55420040 3.6 36900 10229.3 16:49:46.456 INFO ProgressMeter - chr16:56833149 3.8 41810 11054.8 16:49:56.569 INFO ProgressMeter - chr16:56841339 4.0 41850 10593.2 16:50:06.571 INFO ProgressMeter - chr16:59522171 4.1 51250 12447.4 16:50:16.601 INFO ProgressMeter - chr16:64524759 4.3 68430 15971.5 16:50:26.610 INFO ProgressMeter - chr16:67188155 4.5 77680 17451.0 16:50:36.611 INFO ProgressMeter - chr16:67747322 4.6 79670 17252.1 16:50:53.650 INFO ProgressMeter - chr16:68822319 4.9 83460 17025.8 16:51:03.651 INFO ProgressMeter - chr16:69220873 5.1 84870 16744.0 16:51:13.655 INFO ProgressMeter - chr16:73708299 5.2 100490 19194.3 16:51:23.711 INFO ProgressMeter - chr16:77776044 5.4 114590 21208.6 16:51:26.389 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.11083480300000001 16:51:26.389 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 89.32348699100001 16:51:26.389 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 87.11 sec 16:51:26.390 INFO Mutect2 - Shutting down engine [October 8, 2018 4:51:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 5.65 minutes. Runtime.totalMemory()=2136997888 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr16 start:158173608 stop:158173663 contigLength:90338345 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-38/inputs/1547804351/0038-scattered.intervals -O output.vcf Job Mutect2.M2:9:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/tmp.d8598d85 16:44:56.323 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:44:57.322 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.322 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:44:57.322 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:44:57.323 INFO GetSampleName - Executing as root@f3d4c0c6fdaf on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:44:57.323 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:44:57.323 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:56 PM UTC 16:44:57.323 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.323 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.324 INFO GetSampleName - HTSJDK Version: 2.16.0 16:44:57.324 INFO GetSampleName - Picard Version: 2.18.7 16:44:57.324 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:44:57.324 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:44:57.324 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:44:57.324 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:44:57.324 INFO GetSampleName - Deflater: IntelDeflater 16:44:57.324 INFO GetSampleName - Inflater: IntelInflater 16:44:57.324 INFO GetSampleName - GCS max retries/reopens: 20 16:44:57.325 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:44:57.363 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:44:57.363 INFO GetSampleName - Initializing engine 16:45:03.823 INFO GetSampleName - Done initializing engine 16:45:03.887 INFO ProgressMeter - Starting traversal 16:45:03.888 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:03.892 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:03.892 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:03.892 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:03 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1775239168 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/tmp.d8598d85 16:45:21.079 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:21.913 INFO GetSampleName - ------------------------------------------------------------ 16:45:21.913 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:21.913 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:21.921 INFO GetSampleName - Executing as root@f3d4c0c6fdaf on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:21.922 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:21.922 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:20 PM UTC 16:45:21.922 INFO GetSampleName - ------------------------------------------------------------ 16:45:21.922 INFO GetSampleName - ------------------------------------------------------------ 16:45:21.923 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:21.923 INFO GetSampleName - Picard Version: 2.18.7 16:45:21.923 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:21.923 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:21.923 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:21.923 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:21.924 INFO GetSampleName - Deflater: IntelDeflater 16:45:21.924 INFO GetSampleName - Inflater: IntelInflater 16:45:21.924 INFO GetSampleName - GCS max retries/reopens: 20 16:45:21.924 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:21.924 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:21.924 INFO GetSampleName - Initializing engine 16:45:27.683 INFO GetSampleName - Done initializing engine 16:45:27.736 INFO ProgressMeter - Starting traversal 16:45:27.736 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:27.737 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:27.738 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:27.738 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:27 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1801977856 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/tmp.d8598d85 16:45:46.307 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:47.436 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.436 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:47.436 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:47.437 INFO Mutect2 - Executing as root@f3d4c0c6fdaf on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:47.437 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:47.437 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:45 PM UTC 16:45:47.437 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.437 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.462 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:47.462 INFO Mutect2 - Picard Version: 2.18.7 16:45:47.462 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:47.462 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:47.462 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:47.462 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:47.463 INFO Mutect2 - Deflater: IntelDeflater 16:45:47.463 INFO Mutect2 - Inflater: IntelInflater 16:45:47.463 INFO Mutect2 - GCS max retries/reopens: 20 16:45:47.463 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:47.463 INFO Mutect2 - Initializing engine 16:45:54.851 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:57.106 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:57.349 INFO Mutect2 - Done initializing engine 16:45:57.644 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:45:57.663 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:45:57.819 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:45:57.820 INFO IntelPairHmm - Available threads: 24 16:45:57.820 INFO IntelPairHmm - Requested threads: 4 16:45:57.820 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:45:58.965 INFO ProgressMeter - Starting traversal 16:45:58.965 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:09.554 INFO ProgressMeter - chr3:88066625 0.2 330 1870.0 16:46:20.023 INFO ProgressMeter - chr3:88336206 0.4 1270 3618.6 16:46:30.029 INFO ProgressMeter - chr3:88566193 0.5 2070 3998.2 16:46:40.213 INFO ProgressMeter - chr3:88875737 0.7 3140 4567.6 16:46:51.872 INFO ProgressMeter - chr3:89107829 0.9 3940 4468.2 16:47:06.115 INFO ProgressMeter - chr3:89209793 1.1 4290 3833.2 16:47:34.847 INFO ProgressMeter - chr3:89210952 1.6 4300 2690.8 16:48:06.766 INFO ProgressMeter - chr3:89342434 2.1 4760 2234.7 16:48:27.315 INFO ProgressMeter - chr3:89410632 2.5 5000 2022.2 16:48:49.711 INFO ProgressMeter - chr3:89429030 2.8 5070 1781.6 16:48:59.856 INFO ProgressMeter - chr3:89473356 3.0 5230 1734.9 16:49:09.847 INFO ProgressMeter - chr3:93070033 3.2 17510 5503.9 16:49:31.553 INFO ProgressMeter - chr3:93471440 3.5 18850 5320.2 16:49:41.756 INFO ProgressMeter - chr3:96861616 3.7 30610 8243.6 16:49:51.792 INFO ProgressMeter - chr3:99788141 3.9 40730 10497.5 16:50:01.768 INFO ProgressMeter - chr3:103482984 4.0 53550 13233.0 16:50:04.034 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.15485146600000002 16:50:04.034 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 103.05775884900001 16:50:04.035 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 25.55 sec 16:50:04.036 INFO Mutect2 - Shutting down engine [October 8, 2018 4:50:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 4.30 minutes. Runtime.totalMemory()=1992294400 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr3 start:198397545 stop:198397652 contigLength:198295559 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-9/inputs/1547804351/0009-scattered.intervals -O output.vcf Job Mutect2.M2:23:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/tmp.a25a293a 16:45:04.351 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:06.309 INFO GetSampleName - ------------------------------------------------------------ 16:45:06.310 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:06.310 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:06.310 INFO GetSampleName - Executing as root@4a4df74f45f2 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:06.310 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:06.310 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:03 PM UTC 16:45:06.310 INFO GetSampleName - ------------------------------------------------------------ 16:45:06.310 INFO GetSampleName - ------------------------------------------------------------ 16:45:06.338 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:06.338 INFO GetSampleName - Picard Version: 2.18.7 16:45:06.338 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:06.338 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:06.338 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:06.338 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:06.338 INFO GetSampleName - Deflater: IntelDeflater 16:45:06.338 INFO GetSampleName - Inflater: IntelInflater 16:45:06.338 INFO GetSampleName - GCS max retries/reopens: 20 16:45:06.338 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:06.339 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:06.339 INFO GetSampleName - Initializing engine 16:45:11.832 INFO GetSampleName - Done initializing engine 16:45:11.877 INFO ProgressMeter - Starting traversal 16:45:11.878 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:11.879 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:11.879 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:11.879 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:11 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1804075008 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/tmp.a25a293a 16:45:29.603 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:30.455 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.455 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:30.455 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:30.456 INFO GetSampleName - Executing as root@4a4df74f45f2 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:30.456 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:30.456 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:29 PM UTC 16:45:30.456 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.456 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.457 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:30.457 INFO GetSampleName - Picard Version: 2.18.7 16:45:30.457 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:30.457 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:30.457 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:30.457 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:30.457 INFO GetSampleName - Deflater: IntelDeflater 16:45:30.457 INFO GetSampleName - Inflater: IntelInflater 16:45:30.457 INFO GetSampleName - GCS max retries/reopens: 20 16:45:30.458 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:30.458 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:30.458 INFO GetSampleName - Initializing engine 16:45:36.450 INFO GetSampleName - Done initializing engine 16:45:36.495 INFO ProgressMeter - Starting traversal 16:45:36.496 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:36.497 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:36.497 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:36.497 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:36 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1801977856 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/tmp.a25a293a 16:45:55.950 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:57.078 INFO Mutect2 - ------------------------------------------------------------ 16:45:57.078 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:57.082 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:57.083 INFO Mutect2 - Executing as root@4a4df74f45f2 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:57.083 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:57.084 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:55 PM UTC 16:45:57.084 INFO Mutect2 - ------------------------------------------------------------ 16:45:57.084 INFO Mutect2 - ------------------------------------------------------------ 16:45:57.084 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:57.084 INFO Mutect2 - Picard Version: 2.18.7 16:45:57.084 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:57.085 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:57.096 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:57.096 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:57.096 INFO Mutect2 - Deflater: IntelDeflater 16:45:57.097 INFO Mutect2 - Inflater: IntelInflater 16:45:57.097 INFO Mutect2 - GCS max retries/reopens: 20 16:45:57.097 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:57.097 INFO Mutect2 - Initializing engine 16:46:03.806 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:06.270 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:06.538 INFO Mutect2 - Done initializing engine 16:46:06.972 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:07.114 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:07.313 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:07.313 INFO IntelPairHmm - Available threads: 24 16:46:07.319 INFO IntelPairHmm - Requested threads: 4 16:46:07.319 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:09.090 INFO ProgressMeter - Starting traversal 16:46:09.117 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:19.210 INFO ProgressMeter - chr8:88657289 0.2 110 654.0 16:46:29.356 INFO ProgressMeter - chr8:88861152 0.3 840 2490.2 16:46:39.399 INFO ProgressMeter - chr8:89022018 0.5 1420 2813.6 16:46:49.719 INFO ProgressMeter - chr8:89153015 0.7 1900 2807.7 16:46:59.930 INFO ProgressMeter - chr8:89353775 0.8 2620 3093.7 16:47:10.004 INFO ProgressMeter - chr8:89528771 1.0 3270 3222.4 16:47:20.039 INFO ProgressMeter - chr8:89819733 1.2 4330 3663.2 16:47:30.052 INFO ProgressMeter - chr8:90380535 1.3 6360 4714.9 16:47:40.165 INFO ProgressMeter - chr8:91499422 1.5 10390 6846.9 16:47:50.211 INFO ProgressMeter - chr8:92020306 1.7 12260 7276.4 16:48:00.246 INFO ProgressMeter - chr8:92698511 1.9 14690 7931.4 16:48:18.308 INFO ProgressMeter - chr8:93756659 2.2 18520 8601.2 16:48:28.339 INFO ProgressMeter - chr8:94740679 2.3 22150 9545.9 16:48:38.353 INFO ProgressMeter - chr8:96297280 2.5 27810 11180.9 16:48:48.396 INFO ProgressMeter - chr8:97628966 2.7 32730 12329.3 16:48:58.562 INFO ProgressMeter - chr8:98773260 2.8 36980 13094.5 16:49:08.564 INFO ProgressMeter - chr8:100172293 3.0 42070 14066.5 16:49:18.594 INFO ProgressMeter - chr8:101055863 3.2 45360 14363.8 16:49:28.638 INFO ProgressMeter - chr8:102289122 3.3 49850 14990.9 16:49:57.293 INFO ProgressMeter - chr8:102924232 3.8 52220 13731.6 16:50:10.570 INFO ProgressMeter - chr8:103018976 4.0 52580 13065.9 16:50:11.403 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.10811016400000001 16:50:11.404 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 52.176697051000005 16:50:11.404 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 14.10 sec 16:50:11.404 INFO Mutect2 - Shutting down engine [October 8, 2018 4:50:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 4.26 minutes. Runtime.totalMemory()=2155347968 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr8 start:184831213 stop:184831289 contigLength:145138636 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-23/inputs/1547804351/0023-scattered.intervals -O output.vcf Job Mutect2.M2:18:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/tmp.1e1ba4fa 16:45:06.207 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:06.936 INFO GetSampleName - ------------------------------------------------------------ 16:45:06.947 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:06.947 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:06.948 INFO GetSampleName - Executing as root@8bd11677148a on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:06.948 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:06.948 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:06 PM UTC 16:45:06.948 INFO GetSampleName - ------------------------------------------------------------ 16:45:06.948 INFO GetSampleName - ------------------------------------------------------------ 16:45:06.949 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:06.949 INFO GetSampleName - Picard Version: 2.18.7 16:45:06.949 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:06.949 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:06.949 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:06.949 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:06.949 INFO GetSampleName - Deflater: IntelDeflater 16:45:06.949 INFO GetSampleName - Inflater: IntelInflater 16:45:06.950 INFO GetSampleName - GCS max retries/reopens: 20 16:45:06.976 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:06.976 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:06.976 INFO GetSampleName - Initializing engine 16:45:12.570 INFO GetSampleName - Done initializing engine 16:45:12.607 INFO ProgressMeter - Starting traversal 16:45:12.608 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:12.609 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:12.609 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:12.609 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:12 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1800404992 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/tmp.1e1ba4fa 16:45:29.572 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:30.501 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.502 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:30.502 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:30.502 INFO GetSampleName - Executing as root@8bd11677148a on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:30.502 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:30.502 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:29 PM UTC 16:45:30.503 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.527 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.527 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:30.527 INFO GetSampleName - Picard Version: 2.18.7 16:45:30.528 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:30.528 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:30.528 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:30.528 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:30.528 INFO GetSampleName - Deflater: IntelDeflater 16:45:30.528 INFO GetSampleName - Inflater: IntelInflater 16:45:30.528 INFO GetSampleName - GCS max retries/reopens: 20 16:45:30.528 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:30.528 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:30.528 INFO GetSampleName - Initializing engine 16:45:36.145 INFO GetSampleName - Done initializing engine 16:45:36.220 INFO ProgressMeter - Starting traversal 16:45:36.221 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:36.222 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:36.222 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:36.222 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:36 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1805123584 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/tmp.1e1ba4fa 16:45:54.380 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:55.428 INFO Mutect2 - ------------------------------------------------------------ 16:45:55.428 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:55.428 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:55.429 INFO Mutect2 - Executing as root@8bd11677148a on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:55.429 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:55.429 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:54 PM UTC 16:45:55.429 INFO Mutect2 - ------------------------------------------------------------ 16:45:55.429 INFO Mutect2 - ------------------------------------------------------------ 16:45:55.443 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:55.443 INFO Mutect2 - Picard Version: 2.18.7 16:45:55.443 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:55.443 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:55.443 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:55.443 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:55.443 INFO Mutect2 - Deflater: IntelDeflater 16:45:55.443 INFO Mutect2 - Inflater: IntelInflater 16:45:55.444 INFO Mutect2 - GCS max retries/reopens: 20 16:45:55.444 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:55.444 INFO Mutect2 - Initializing engine 16:46:01.736 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:04.007 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:04.264 INFO Mutect2 - Done initializing engine 16:46:04.621 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:04.771 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:04.921 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:04.922 INFO IntelPairHmm - Available threads: 24 16:46:04.922 INFO IntelPairHmm - Requested threads: 4 16:46:04.922 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:06.259 INFO ProgressMeter - Starting traversal 16:46:06.260 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:16.367 INFO ProgressMeter - chr6:97127594 0.2 280 1662.4 16:46:26.710 INFO ProgressMeter - chr6:97274648 0.3 800 2347.3 16:46:36.796 INFO ProgressMeter - chr6:97499901 0.5 1590 3124.3 16:46:46.809 INFO ProgressMeter - chr6:97673429 0.7 2200 3255.4 16:46:56.960 INFO ProgressMeter - chr6:97895449 0.8 2980 3526.6 16:47:06.986 INFO ProgressMeter - chr6:98182041 1.0 3990 3942.4 16:47:17.041 INFO ProgressMeter - chr6:98776960 1.2 6060 5137.0 16:47:27.131 INFO ProgressMeter - chr6:99463149 1.3 8480 6291.5 16:48:13.127 INFO ProgressMeter - chr6:100051368 2.1 10530 4980.0 16:48:23.204 INFO ProgressMeter - chr6:102116687 2.3 17750 7776.9 16:48:25.564 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.07323112200000001 16:48:25.564 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 27.116353825 16:48:25.564 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 13.22 sec 16:48:25.565 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.52 minutes. Runtime.totalMemory()=1861222400 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr6 start:185040350 stop:185040399 contigLength:170805979 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-18/inputs/1547804351/0018-scattered.intervals -O output.vcf Job Mutect2.M2:6:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/tmp.bf92be98 16:45:11.557 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:12.352 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.352 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:12.352 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:12.355 INFO GetSampleName - Executing as root@88acf3397fcd on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:12.356 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:12.356 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:11 PM UTC 16:45:12.356 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.356 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.357 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:12.357 INFO GetSampleName - Picard Version: 2.18.7 16:45:12.357 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:12.357 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:12.357 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:12.357 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:12.357 INFO GetSampleName - Deflater: IntelDeflater 16:45:12.357 INFO GetSampleName - Inflater: IntelInflater 16:45:12.357 INFO GetSampleName - GCS max retries/reopens: 20 16:45:12.357 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:12.358 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:12.358 INFO GetSampleName - Initializing engine 16:45:17.926 INFO GetSampleName - Done initializing engine 16:45:18.018 INFO ProgressMeter - Starting traversal 16:45:18.019 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:18.020 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:18.020 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:18.020 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1768423424 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/tmp.bf92be98 16:45:36.100 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:37.568 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.569 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:37.569 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:37.569 INFO GetSampleName - Executing as root@88acf3397fcd on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:37.569 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:37.570 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:35 PM UTC 16:45:37.570 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.570 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.570 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:37.570 INFO GetSampleName - Picard Version: 2.18.7 16:45:37.598 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:37.598 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:37.598 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:37.598 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:37.598 INFO GetSampleName - Deflater: IntelDeflater 16:45:37.599 INFO GetSampleName - Inflater: IntelInflater 16:45:37.599 INFO GetSampleName - GCS max retries/reopens: 20 16:45:37.599 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:37.600 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:37.600 INFO GetSampleName - Initializing engine 16:45:43.536 INFO GetSampleName - Done initializing engine 16:45:43.596 INFO ProgressMeter - Starting traversal 16:45:43.597 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:43.598 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:43.598 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:43.598 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:43 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1814036480 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/tmp.bf92be98 16:46:02.785 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:03.895 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.895 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:03.895 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:03.896 INFO Mutect2 - Executing as root@88acf3397fcd on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:03.896 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:03.896 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:02 PM UTC 16:46:03.896 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.896 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.897 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:03.897 INFO Mutect2 - Picard Version: 2.18.7 16:46:03.897 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:03.897 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:03.897 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:03.897 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:03.897 INFO Mutect2 - Deflater: IntelDeflater 16:46:03.897 INFO Mutect2 - Inflater: IntelInflater 16:46:03.897 INFO Mutect2 - GCS max retries/reopens: 20 16:46:03.897 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:03.927 INFO Mutect2 - Initializing engine 16:46:10.059 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:12.348 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:12.625 INFO Mutect2 - Done initializing engine 16:46:13.010 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:13.024 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:13.204 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:13.205 INFO IntelPairHmm - Available threads: 24 16:46:13.205 INFO IntelPairHmm - Requested threads: 4 16:46:13.205 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:14.510 INFO ProgressMeter - Starting traversal 16:46:14.511 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:24.889 INFO ProgressMeter - chr2:137222140 0.2 340 1972.3 16:46:28.747 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.044588169000000004 16:46:28.747 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.294967542 16:46:28.747 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.43 sec 16:46:28.760 INFO Mutect2 - Shutting down engine [October 8, 2018 4:46:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.44 minutes. Runtime.totalMemory()=1862270976 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr2 start:245325358 stop:245325403 contigLength:242193529 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-6/inputs/1547804351/0006-scattered.intervals -O output.vcf Job Mutect2.M2:12:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/tmp.d229ec4f 16:45:11.717 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:12.604 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.604 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:12.609 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:12.612 INFO GetSampleName - Executing as root@335c837442fc on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:12.612 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:12.612 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:11 PM UTC 16:45:12.612 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.612 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.613 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:12.613 INFO GetSampleName - Picard Version: 2.18.7 16:45:12.613 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:12.613 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:12.613 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:12.613 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:12.613 INFO GetSampleName - Deflater: IntelDeflater 16:45:12.614 INFO GetSampleName - Inflater: IntelInflater 16:45:12.614 INFO GetSampleName - GCS max retries/reopens: 20 16:45:12.614 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:12.614 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:12.614 INFO GetSampleName - Initializing engine 16:45:18.643 INFO GetSampleName - Done initializing engine 16:45:18.705 INFO ProgressMeter - Starting traversal 16:45:18.706 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:18.707 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:18.707 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:18.707 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1725956096 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/tmp.d229ec4f 16:45:36.449 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:37.264 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.264 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:37.264 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:37.264 INFO GetSampleName - Executing as root@335c837442fc on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:37.265 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:37.278 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:36 PM UTC 16:45:37.278 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.278 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.279 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:37.279 INFO GetSampleName - Picard Version: 2.18.7 16:45:37.279 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:37.279 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:37.282 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:37.282 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:37.282 INFO GetSampleName - Deflater: IntelDeflater 16:45:37.282 INFO GetSampleName - Inflater: IntelInflater 16:45:37.282 INFO GetSampleName - GCS max retries/reopens: 20 16:45:37.282 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:37.291 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:37.291 INFO GetSampleName - Initializing engine 16:45:43.766 INFO GetSampleName - Done initializing engine 16:45:43.820 INFO ProgressMeter - Starting traversal 16:45:43.821 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:43.822 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:43.824 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:43.824 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:43 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1795686400 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/tmp.d229ec4f 16:46:02.948 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:03.996 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.996 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:03.996 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:03.996 INFO Mutect2 - Executing as root@335c837442fc on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:03.997 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:04.007 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:02 PM UTC 16:46:04.007 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.007 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.007 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:04.007 INFO Mutect2 - Picard Version: 2.18.7 16:46:04.007 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:04.008 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:04.008 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:04.008 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:04.008 INFO Mutect2 - Deflater: IntelDeflater 16:46:04.008 INFO Mutect2 - Inflater: IntelInflater 16:46:04.008 INFO Mutect2 - GCS max retries/reopens: 20 16:46:04.008 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:04.008 INFO Mutect2 - Initializing engine 16:46:11.802 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:14.208 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:14.526 INFO Mutect2 - Done initializing engine 16:46:14.976 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:14.996 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:15.168 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:15.169 INFO IntelPairHmm - Available threads: 24 16:46:15.169 INFO IntelPairHmm - Requested threads: 4 16:46:15.169 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:16.432 INFO ProgressMeter - Starting traversal 16:46:16.433 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:26.699 INFO ProgressMeter - chr4:82791061 0.2 260 1531.8 16:46:36.697 INFO ProgressMeter - chr4:83153575 0.3 1510 4471.0 16:46:46.930 INFO ProgressMeter - chr4:83352659 0.5 2200 4328.3 16:46:57.070 INFO ProgressMeter - chr4:83663008 0.7 3280 4842.9 16:47:07.073 INFO ProgressMeter - chr4:84008866 0.8 4480 5308.2 16:47:17.101 INFO ProgressMeter - chr4:84276071 1.0 5400 5342.0 16:47:27.090 INFO ProgressMeter - chr4:85162173 1.2 8440 7167.0 16:47:37.129 INFO ProgressMeter - chr4:85951524 1.3 11170 8305.2 16:47:47.158 INFO ProgressMeter - chr4:88072956 1.5 18490 12228.2 16:48:00.229 INFO ProgressMeter - chr4:88731455 1.7 20760 12000.5 16:48:10.290 INFO ProgressMeter - chr4:91001591 1.9 28560 15053.8 16:48:20.296 INFO ProgressMeter - chr4:93722584 2.1 37880 18349.3 16:48:30.297 INFO ProgressMeter - chr4:96584857 2.2 47750 21402.3 16:48:42.887 INFO ProgressMeter - chr4:98025310 2.4 52720 21598.6 16:48:52.888 INFO ProgressMeter - chr4:99312699 2.6 57150 21917.0 16:49:07.428 INFO ProgressMeter - chr4:102664632 2.8 68700 24106.0 16:49:20.858 INFO ProgressMeter - chr4:105234134 3.1 77550 25229.8 16:49:33.176 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.169045839 16:49:33.177 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 40.216362567000004 16:49:33.177 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 12.17 sec 16:49:33.178 INFO Mutect2 - Shutting down engine [October 8, 2018 4:49:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 3.51 minutes. Runtime.totalMemory()=2119696384 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr4 start:207440304 stop:207440347 contigLength:190214555 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-12/inputs/1547804351/0012-scattered.intervals -O output.vcf Job Mutect2.M2:43:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/tmp.8c640e09 16:44:58.992 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:00.923 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.931 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:00.931 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:00.972 INFO GetSampleName - Executing as root@50b130ff3369 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:00.972 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:00.972 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:58 PM UTC 16:45:00.973 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.973 INFO GetSampleName - ------------------------------------------------------------ 16:45:00.973 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:00.973 INFO GetSampleName - Picard Version: 2.18.7 16:45:00.973 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:00.973 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:00.974 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:00.974 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:00.974 INFO GetSampleName - Deflater: IntelDeflater 16:45:00.997 INFO GetSampleName - Inflater: IntelInflater 16:45:00.997 INFO GetSampleName - GCS max retries/reopens: 20 16:45:00.997 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:00.998 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:00.998 INFO GetSampleName - Initializing engine 16:45:07.012 INFO GetSampleName - Done initializing engine 16:45:07.072 INFO ProgressMeter - Starting traversal 16:45:07.073 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:07.074 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:07.074 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:07.074 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:07 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=1721237504 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/tmp.8c640e09 16:45:24.945 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:25.795 INFO GetSampleName - ------------------------------------------------------------ 16:45:25.795 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:25.795 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:25.795 INFO GetSampleName - Executing as root@50b130ff3369 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:25.795 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:25.796 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:24 PM UTC 16:45:25.796 INFO GetSampleName - ------------------------------------------------------------ 16:45:25.796 INFO GetSampleName - ------------------------------------------------------------ 16:45:25.796 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:25.796 INFO GetSampleName - Picard Version: 2.18.7 16:45:25.796 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:25.797 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:25.797 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:25.797 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:25.797 INFO GetSampleName - Deflater: IntelDeflater 16:45:25.797 INFO GetSampleName - Inflater: IntelInflater 16:45:25.797 INFO GetSampleName - GCS max retries/reopens: 20 16:45:25.797 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:25.797 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:25.797 INFO GetSampleName - Initializing engine 16:45:31.952 INFO GetSampleName - Done initializing engine 16:45:32.021 INFO ProgressMeter - Starting traversal 16:45:32.022 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:32.023 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:32.023 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:32.023 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:32 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1765277696 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/tmp.8c640e09 16:45:51.807 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:53.570 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.570 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:53.573 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:53.573 INFO Mutect2 - Executing as root@50b130ff3369 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:53.573 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:53.573 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:51 PM UTC 16:45:53.573 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.574 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.574 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:53.574 INFO Mutect2 - Picard Version: 2.18.7 16:45:53.574 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:53.574 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:53.575 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:53.575 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:53.575 INFO Mutect2 - Deflater: IntelDeflater 16:45:53.575 INFO Mutect2 - Inflater: IntelInflater 16:45:53.575 INFO Mutect2 - GCS max retries/reopens: 20 16:45:53.575 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:53.575 INFO Mutect2 - Initializing engine 16:46:00.138 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:02.373 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:02.680 INFO Mutect2 - Done initializing engine 16:46:03.029 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:03.052 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:03.204 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:03.204 INFO IntelPairHmm - Available threads: 24 16:46:03.204 INFO IntelPairHmm - Requested threads: 4 16:46:03.204 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:04.421 INFO ProgressMeter - Starting traversal 16:46:04.422 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:14.441 INFO ProgressMeter - chr20:53999695 0.2 390 2335.8 16:46:24.487 INFO ProgressMeter - chr20:54188378 0.3 1060 3175.2 16:46:34.521 INFO ProgressMeter - chr20:54344332 0.5 1610 3209.4 16:46:44.711 INFO ProgressMeter - chr20:54520123 0.7 2230 3321.0 16:46:55.089 INFO ProgressMeter - chr20:54847144 0.8 3360 3978.9 16:47:05.243 INFO ProgressMeter - chr20:55057618 1.0 4110 4056.6 16:47:15.250 INFO ProgressMeter - chr20:55430446 1.2 5400 4574.5 16:47:25.261 INFO ProgressMeter - chr20:56325360 1.3 8530 6331.1 16:47:41.558 INFO ProgressMeter - chr20:56372741 1.6 8700 5374.0 16:47:50.659 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.104140989 16:47:50.659 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 15.936567285 16:47:50.659 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 7.22 sec 16:47:50.661 INFO Mutect2 - Shutting down engine [October 8, 2018 4:47:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 1.98 minutes. Runtime.totalMemory()=2113929216 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr20 start:98134871 stop:98134946 contigLength:64444167 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-43/inputs/1547804351/0043-scattered.intervals -O output.vcf Job Mutect2.M2:29:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/tmp.64d3be76 16:45:12.596 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:13.488 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.488 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:13.489 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:13.489 INFO GetSampleName - Executing as root@dc447ef177b7 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:13.489 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:13.489 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:12 PM UTC 16:45:13.489 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.489 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.490 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:13.490 INFO GetSampleName - Picard Version: 2.18.7 16:45:13.490 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:13.490 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:13.491 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:13.491 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:13.491 INFO GetSampleName - Deflater: IntelDeflater 16:45:13.491 INFO GetSampleName - Inflater: IntelInflater 16:45:13.491 INFO GetSampleName - GCS max retries/reopens: 20 16:45:13.491 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:13.491 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:13.491 INFO GetSampleName - Initializing engine 16:45:19.903 INFO GetSampleName - Done initializing engine 16:45:19.984 INFO ProgressMeter - Starting traversal 16:45:19.984 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:19.986 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:19.986 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:19.986 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1813512192 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/tmp.64d3be76 16:45:36.981 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:37.811 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.811 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:37.811 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:37.811 INFO GetSampleName - Executing as root@dc447ef177b7 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:37.812 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:37.812 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:36 PM UTC 16:45:37.812 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.812 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.834 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:37.834 INFO GetSampleName - Picard Version: 2.18.7 16:45:37.834 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:37.834 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:37.834 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:37.834 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:37.834 INFO GetSampleName - Deflater: IntelDeflater 16:45:37.835 INFO GetSampleName - Inflater: IntelInflater 16:45:37.835 INFO GetSampleName - GCS max retries/reopens: 20 16:45:37.835 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:37.835 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:37.835 INFO GetSampleName - Initializing engine 16:45:43.359 INFO GetSampleName - Done initializing engine 16:45:43.454 INFO ProgressMeter - Starting traversal 16:45:43.455 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:43.456 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:43.456 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:43.456 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:43 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1781006336 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/tmp.64d3be76 16:46:02.229 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:03.423 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.424 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:03.424 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:03.430 INFO Mutect2 - Executing as root@dc447ef177b7 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:03.431 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:03.431 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:01 PM UTC 16:46:03.431 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.431 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.432 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:03.432 INFO Mutect2 - Picard Version: 2.18.7 16:46:03.432 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:03.432 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:03.433 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:03.433 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:03.433 INFO Mutect2 - Deflater: IntelDeflater 16:46:03.433 INFO Mutect2 - Inflater: IntelInflater 16:46:03.433 INFO Mutect2 - GCS max retries/reopens: 20 16:46:03.433 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:03.433 INFO Mutect2 - Initializing engine 16:46:10.083 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:12.069 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:12.325 INFO Mutect2 - Done initializing engine 16:46:12.768 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:12.802 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:12.931 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:12.931 INFO IntelPairHmm - Available threads: 24 16:46:12.931 INFO IntelPairHmm - Requested threads: 4 16:46:12.932 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:13.969 INFO ProgressMeter - Starting traversal 16:46:13.970 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:24.325 INFO ProgressMeter - chr11:57471037 0.2 320 1854.4 16:46:35.072 INFO ProgressMeter - chr11:57651134 0.4 960 2736.3 16:46:45.033 INFO ProgressMeter - chr11:57828068 0.5 1590 3071.2 16:46:55.283 INFO ProgressMeter - chr11:58022265 0.7 2270 3296.8 16:47:18.299 INFO ProgressMeter - chr11:58242375 1.1 3030 2826.1 16:47:54.382 INFO ProgressMeter - chr11:58244490 1.7 3040 1816.5 16:48:04.391 INFO ProgressMeter - chr11:59583695 1.8 7700 4184.0 16:48:14.406 INFO ProgressMeter - chr11:61427346 2.0 14140 7044.4 16:48:26.170 INFO ProgressMeter - chr11:62330840 2.2 17350 7874.4 16:48:49.660 INFO ProgressMeter - chr11:62332714 2.6 17360 6690.3 16:48:59.701 INFO ProgressMeter - chr11:64221512 2.8 24030 8699.7 16:49:09.712 INFO ProgressMeter - chr11:65054786 2.9 27050 9235.1 16:49:19.718 INFO ProgressMeter - chr11:67409931 3.1 35480 11460.7 16:49:29.790 INFO ProgressMeter - chr11:69775511 3.3 43920 13457.3 16:49:56.304 INFO ProgressMeter - chr11:72282081 3.7 52840 14259.7 16:50:06.315 INFO ProgressMeter - chr11:74865021 3.9 61960 16000.3 16:50:24.999 INFO ProgressMeter - chr11:75079883 4.2 62710 14988.7 16:50:38.897 INFO ProgressMeter - chr11:76462495 4.4 67590 15307.7 16:50:51.943 INFO ProgressMeter - chr11:76464757 4.6 67600 14591.3 16:51:02.008 INFO ProgressMeter - chr11:76497540 4.8 67720 14106.5 16:51:12.678 INFO ProgressMeter - chr11:76543952 5.0 67900 13638.7 16:51:23.833 INFO ProgressMeter - chr11:76546985 5.2 67920 13151.6 16:51:37.115 INFO ProgressMeter - chr11:78104839 5.4 73450 13637.8 16:51:47.116 INFO ProgressMeter - chr11:83070067 5.6 90730 16340.6 16:51:57.130 INFO ProgressMeter - chr11:87168088 5.7 105000 18358.8 16:52:07.131 INFO ProgressMeter - chr11:93159043 5.9 125700 21355.7 16:52:13.062 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.153212088 16:52:13.063 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 130.281617927 16:52:13.063 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 51.39 sec 16:52:13.064 INFO Mutect2 - Shutting down engine [October 8, 2018 4:52:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 6.19 minutes. Runtime.totalMemory()=2104492032 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr11 start:145099650 stop:145099729 contigLength:135086622 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-29/inputs/1547804351/0029-scattered.intervals -O output.vcf Job Mutect2.M2:32:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/tmp.dd71d0e2 16:44:55.912 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:44:57.171 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.171 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:44:57.172 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:44:57.172 INFO GetSampleName - Executing as root@4f28cbc090fb on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:44:57.182 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:44:57.182 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:55 PM UTC 16:44:57.183 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.183 INFO GetSampleName - ------------------------------------------------------------ 16:44:57.183 INFO GetSampleName - HTSJDK Version: 2.16.0 16:44:57.184 INFO GetSampleName - Picard Version: 2.18.7 16:44:57.184 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:44:57.184 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:44:57.184 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:44:57.184 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:44:57.184 INFO GetSampleName - Deflater: IntelDeflater 16:44:57.184 INFO GetSampleName - Inflater: IntelInflater 16:44:57.184 INFO GetSampleName - GCS max retries/reopens: 20 16:44:57.184 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:44:57.185 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:44:57.185 INFO GetSampleName - Initializing engine 16:45:03.498 INFO GetSampleName - Done initializing engine 16:45:03.542 INFO ProgressMeter - Starting traversal 16:45:03.543 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:03.544 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:03.545 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:03.545 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:03 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1772617728 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/tmp.dd71d0e2 16:45:20.826 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:21.651 INFO GetSampleName - ------------------------------------------------------------ 16:45:21.652 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:21.652 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:21.652 INFO GetSampleName - Executing as root@4f28cbc090fb on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:21.652 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:21.652 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:20 PM UTC 16:45:21.652 INFO GetSampleName - ------------------------------------------------------------ 16:45:21.684 INFO GetSampleName - ------------------------------------------------------------ 16:45:21.684 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:21.684 INFO GetSampleName - Picard Version: 2.18.7 16:45:21.684 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:21.685 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:21.685 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:21.685 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:21.685 INFO GetSampleName - Deflater: IntelDeflater 16:45:21.685 INFO GetSampleName - Inflater: IntelInflater 16:45:21.685 INFO GetSampleName - GCS max retries/reopens: 20 16:45:21.685 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:21.685 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:21.685 INFO GetSampleName - Initializing engine 16:45:27.828 INFO GetSampleName - Done initializing engine 16:45:27.896 INFO ProgressMeter - Starting traversal 16:45:27.897 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:27.899 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:27.899 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:27.899 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:27 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1744830464 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/tmp.dd71d0e2 16:45:46.515 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:47.661 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.661 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:47.662 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:47.662 INFO Mutect2 - Executing as root@4f28cbc090fb on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:47.662 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:47.662 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:46 PM UTC 16:45:47.662 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.662 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.677 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:47.677 INFO Mutect2 - Picard Version: 2.18.7 16:45:47.677 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:47.677 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:47.677 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:47.678 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:47.678 INFO Mutect2 - Deflater: IntelDeflater 16:45:47.678 INFO Mutect2 - Inflater: IntelInflater 16:45:47.678 INFO Mutect2 - GCS max retries/reopens: 20 16:45:47.678 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:47.678 INFO Mutect2 - Initializing engine 16:45:54.451 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:56.842 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:57.247 INFO Mutect2 - Done initializing engine 16:45:57.650 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:45:57.688 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:45:57.898 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:45:57.899 INFO IntelPairHmm - Available threads: 24 16:45:57.899 INFO IntelPairHmm - Requested threads: 4 16:45:57.899 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:45:59.337 INFO ProgressMeter - Starting traversal 16:45:59.338 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:09.815 INFO ProgressMeter - chr12:115452928 0.2 410 2353.2 16:46:19.800 INFO ProgressMeter - chr12:115679666 0.3 1200 3518.7 16:46:30.056 INFO ProgressMeter - chr12:115854414 0.5 1810 3535.4 16:46:40.626 INFO ProgressMeter - chr12:116058071 0.7 2520 3662.2 16:46:50.635 INFO ProgressMeter - chr12:116345505 0.9 3510 4105.5 16:47:00.731 INFO ProgressMeter - chr12:116536028 1.0 4190 4094.9 16:47:11.021 INFO ProgressMeter - chr12:116700185 1.2 4770 3992.7 16:47:28.437 INFO ProgressMeter - chr12:116755594 1.5 4970 3346.8 16:47:51.507 INFO ProgressMeter - chr12:116758428 1.9 4980 2663.8 16:48:01.543 INFO ProgressMeter - chr12:117802822 2.0 8640 4242.1 16:48:11.668 INFO ProgressMeter - chr12:119329157 2.2 14050 6370.4 16:48:21.831 INFO ProgressMeter - chr12:120990198 2.4 19980 8413.0 16:48:32.976 INFO ProgressMeter - chr12:120999479 2.6 20020 7818.4 16:48:47.590 INFO ProgressMeter - chr12:122366288 2.8 24940 8893.8 16:48:56.195 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.102179613 16:48:56.195 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 33.98677571 16:48:56.195 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 18.01 sec 16:48:56.196 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 3.16 minutes. Runtime.totalMemory()=2127560704 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr12 start:169398154 stop:169398215 contigLength:133275309 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-32/inputs/1547804351/0032-scattered.intervals -O output.vcf Job Mutect2.M2:16:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/tmp.5fb5cb9f 16:45:00.237 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:02.424 INFO GetSampleName - ------------------------------------------------------------ 16:45:02.455 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:02.471 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:02.472 INFO GetSampleName - Executing as root@6f5f0a4bbed6 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:02.472 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:02.472 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:59 PM UTC 16:45:02.472 INFO GetSampleName - ------------------------------------------------------------ 16:45:02.472 INFO GetSampleName - ------------------------------------------------------------ 16:45:02.473 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:02.473 INFO GetSampleName - Picard Version: 2.18.7 16:45:02.473 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:02.473 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:02.473 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:02.473 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:02.496 INFO GetSampleName - Deflater: IntelDeflater 16:45:02.496 INFO GetSampleName - Inflater: IntelInflater 16:45:02.496 INFO GetSampleName - GCS max retries/reopens: 20 16:45:02.496 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:02.496 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:02.497 INFO GetSampleName - Initializing engine 16:45:09.625 INFO GetSampleName - Done initializing engine 16:45:09.645 INFO ProgressMeter - Starting traversal 16:45:09.646 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:09.647 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:09.647 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:09.647 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:09 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.17 minutes. Runtime.totalMemory()=1829240832 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/tmp.5fb5cb9f 16:45:27.212 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:28.186 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.186 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:28.186 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:28.187 INFO GetSampleName - Executing as root@6f5f0a4bbed6 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:28.187 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:28.187 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:26 PM UTC 16:45:28.187 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.187 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.188 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:28.188 INFO GetSampleName - Picard Version: 2.18.7 16:45:28.188 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:28.188 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:28.188 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:28.188 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:28.189 INFO GetSampleName - Deflater: IntelDeflater 16:45:28.189 INFO GetSampleName - Inflater: IntelInflater 16:45:28.189 INFO GetSampleName - GCS max retries/reopens: 20 16:45:28.189 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:28.189 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:28.189 INFO GetSampleName - Initializing engine 16:45:34.888 INFO GetSampleName - Done initializing engine 16:45:34.947 INFO ProgressMeter - Starting traversal 16:45:34.948 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:34.949 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:34.949 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:34.950 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:34 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1767899136 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/tmp.5fb5cb9f 16:45:53.126 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:53.959 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.959 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:53.959 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:53.960 INFO Mutect2 - Executing as root@6f5f0a4bbed6 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:53.960 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:53.960 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:53 PM UTC 16:45:53.960 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.960 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.961 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:53.961 INFO Mutect2 - Picard Version: 2.18.7 16:45:53.961 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:53.961 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:53.961 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:53.961 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:53.961 INFO Mutect2 - Deflater: IntelDeflater 16:45:53.961 INFO Mutect2 - Inflater: IntelInflater 16:45:53.962 INFO Mutect2 - GCS max retries/reopens: 20 16:45:53.991 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:53.991 INFO Mutect2 - Initializing engine 16:46:00.532 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:02.589 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:02.891 INFO Mutect2 - Done initializing engine 16:46:03.333 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:03.345 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:03.498 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:03.499 INFO IntelPairHmm - Available threads: 24 16:46:03.499 INFO IntelPairHmm - Requested threads: 4 16:46:03.499 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:04.431 INFO ProgressMeter - Starting traversal 16:46:04.432 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:14.939 INFO ProgressMeter - chr5:149954660 0.2 230 1314.2 16:46:34.758 INFO ProgressMeter - chr5:150055973 0.5 590 1167.3 16:46:56.820 INFO ProgressMeter - chr5:150062424 0.9 620 710.1 16:47:21.972 INFO ProgressMeter - chr5:150077390 1.3 680 526.2 16:47:32.080 INFO ProgressMeter - chr5:150212007 1.5 1180 807.8 16:47:42.083 INFO ProgressMeter - chr5:150678894 1.6 2870 1763.4 16:47:43.227 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.096820053 16:47:43.228 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 33.621970028 16:47:43.228 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 15.09 sec 16:47:43.230 INFO Mutect2 - Shutting down engine [October 8, 2018 4:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 1.84 minutes. Runtime.totalMemory()=1888485376 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr5 start:263264286 stop:263264340 contigLength:181538259 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-16/inputs/1547804351/0016-scattered.intervals -O output.vcf Job Mutect2.M2:39:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/tmp.b666694a 16:44:56.983 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:44:58.243 INFO GetSampleName - ------------------------------------------------------------ 16:44:58.243 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:44:58.243 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:44:58.244 INFO GetSampleName - Executing as root@4e59fb2e266f on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:44:58.252 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:44:58.252 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:56 PM UTC 16:44:58.252 INFO GetSampleName - ------------------------------------------------------------ 16:44:58.252 INFO GetSampleName - ------------------------------------------------------------ 16:44:58.253 INFO GetSampleName - HTSJDK Version: 2.16.0 16:44:58.253 INFO GetSampleName - Picard Version: 2.18.7 16:44:58.253 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:44:58.253 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:44:58.253 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:44:58.253 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:44:58.253 INFO GetSampleName - Deflater: IntelDeflater 16:44:58.253 INFO GetSampleName - Inflater: IntelInflater 16:44:58.254 INFO GetSampleName - GCS max retries/reopens: 20 16:44:58.254 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:44:58.254 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:44:58.254 INFO GetSampleName - Initializing engine 16:45:04.535 INFO GetSampleName - Done initializing engine 16:45:04.575 INFO ProgressMeter - Starting traversal 16:45:04.576 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:04.577 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:04.577 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:04.577 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:04 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1819803648 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/tmp.b666694a 16:45:21.995 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:22.980 INFO GetSampleName - ------------------------------------------------------------ 16:45:22.981 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:22.981 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:22.984 INFO GetSampleName - Executing as root@4e59fb2e266f on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:22.984 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:22.984 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:21 PM UTC 16:45:22.984 INFO GetSampleName - ------------------------------------------------------------ 16:45:22.984 INFO GetSampleName - ------------------------------------------------------------ 16:45:22.985 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:22.985 INFO GetSampleName - Picard Version: 2.18.7 16:45:22.985 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:22.985 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:22.985 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:22.985 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:22.985 INFO GetSampleName - Deflater: IntelDeflater 16:45:22.985 INFO GetSampleName - Inflater: IntelInflater 16:45:22.985 INFO GetSampleName - GCS max retries/reopens: 20 16:45:22.986 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:22.986 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:22.986 INFO GetSampleName - Initializing engine 16:45:28.504 INFO GetSampleName - Done initializing engine 16:45:28.564 INFO ProgressMeter - Starting traversal 16:45:28.565 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:28.566 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:28.567 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:28.567 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:28 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1717043200 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/tmp.b666694a 16:45:46.528 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:47.435 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.435 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:47.450 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:47.451 INFO Mutect2 - Executing as root@4e59fb2e266f on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:47.451 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:47.452 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:46 PM UTC 16:45:47.452 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.452 INFO Mutect2 - ------------------------------------------------------------ 16:45:47.459 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:47.459 INFO Mutect2 - Picard Version: 2.18.7 16:45:47.459 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:47.460 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:47.471 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:47.471 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:47.471 INFO Mutect2 - Deflater: IntelDeflater 16:45:47.471 INFO Mutect2 - Inflater: IntelInflater 16:45:47.471 INFO Mutect2 - GCS max retries/reopens: 20 16:45:47.471 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:47.471 INFO Mutect2 - Initializing engine 16:45:53.646 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:55.687 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:56.169 INFO Mutect2 - Done initializing engine 16:45:56.516 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:45:56.558 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:45:56.715 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:45:56.715 INFO IntelPairHmm - Available threads: 24 16:45:56.715 INFO IntelPairHmm - Requested threads: 4 16:45:56.715 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:45:58.039 INFO ProgressMeter - Starting traversal 16:45:58.040 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:08.114 INFO ProgressMeter - chr17:18894603 0.2 500 2982.4 16:46:18.212 INFO ProgressMeter - chr17:19363520 0.3 2110 6284.4 16:46:28.320 INFO ProgressMeter - chr17:19529145 0.5 2700 5350.1 16:46:38.379 INFO ProgressMeter - chr17:19747624 0.7 3460 5146.4 16:46:48.547 INFO ProgressMeter - chr17:19998596 0.8 4330 5146.8 16:46:58.916 INFO ProgressMeter - chr17:20398764 1.0 5710 5627.8 16:47:09.021 INFO ProgressMeter - chr17:21019279 1.2 7850 6635.6 16:47:46.391 INFO ProgressMeter - chr17:21504770 1.8 9540 5282.8 16:47:58.384 INFO ProgressMeter - chr17:22062057 2.0 11530 5748.6 16:48:08.409 INFO ProgressMeter - chr17:26594979 2.2 26770 12320.4 16:48:18.435 INFO ProgressMeter - chr17:27980051 2.3 31710 13551.8 16:48:28.586 INFO ProgressMeter - chr17:29246295 2.5 36270 14455.4 16:48:55.548 INFO ProgressMeter - chr17:29716786 3.0 37970 12834.4 16:49:22.566 INFO ProgressMeter - chr17:31157406 3.4 43100 12643.9 16:49:44.215 INFO ProgressMeter - chr17:31160303 3.8 43120 11438.9 16:50:08.360 INFO ProgressMeter - chr17:31164912 4.2 43140 10340.4 16:50:18.628 INFO ProgressMeter - chr17:31170825 4.3 43170 9939.8 16:50:58.820 INFO ProgressMeter - chr17:31182381 5.0 43230 8623.6 16:51:39.426 INFO ProgressMeter - chr17:31201257 5.7 43300 7610.2 16:51:49.613 INFO ProgressMeter - chr17:31207394 5.9 43330 7394.8 16:52:01.016 INFO ProgressMeter - chr17:31216390 6.0 43370 7169.1 16:52:21.282 INFO ProgressMeter - chr17:31222572 6.4 43400 6794.7 16:52:42.304 INFO ProgressMeter - chr17:31226103 6.7 43420 6444.3 16:52:53.766 INFO ProgressMeter - chr17:31227418 6.9 43430 6268.1 16:53:13.564 INFO ProgressMeter - chr17:31230108 7.3 43450 5985.9 16:53:37.343 INFO ProgressMeter - chr17:31232160 7.7 43460 5677.3 16:53:58.106 INFO ProgressMeter - chr17:31235630 8.0 43480 5434.3 16:54:18.625 INFO ProgressMeter - chr17:31237825 8.3 43490 5212.7 16:54:38.075 INFO ProgressMeter - chr17:31253785 8.7 43560 5025.8 16:54:48.419 INFO ProgressMeter - chr17:31259438 8.8 43590 4931.2 16:55:04.775 INFO ProgressMeter - chr17:31265536 9.1 43620 4787.0 16:55:19.654 INFO ProgressMeter - chr17:31330878 9.4 43880 4687.9 16:55:36.344 INFO ProgressMeter - chr17:31336968 9.6 43910 4555.7 16:55:48.909 INFO ProgressMeter - chr17:31338301 9.8 43920 4459.9 16:55:59.818 INFO ProgressMeter - chr17:31350579 10.0 43980 4385.0 16:56:15.169 INFO ProgressMeter - chr17:31358288 10.3 44020 4279.8 16:56:34.239 INFO ProgressMeter - chr17:31361819 10.6 44040 4153.4 16:56:45.622 INFO ProgressMeter - chr17:31966346 10.8 46240 4284.2 16:56:55.622 INFO ProgressMeter - chr17:38097650 11.0 68050 6209.1 16:57:08.102 INFO ProgressMeter - chr17:39471297 11.2 72980 6534.9 16:57:18.427 INFO ProgressMeter - chr17:39526651 11.3 73200 6455.2 16:57:29.969 INFO ProgressMeter - chr17:39710265 11.5 73870 6405.6 16:57:41.216 INFO ProgressMeter - chr17:39724959 11.7 73940 6309.1 16:57:54.028 INFO ProgressMeter - chr17:43046581 11.9 85970 7204.3 16:58:08.042 INFO ProgressMeter - chr17:43063749 12.2 86050 7072.6 16:58:20.186 INFO ProgressMeter - chr17:43076621 12.4 86110 6961.7 16:58:44.541 INFO ProgressMeter - chr17:43092149 12.8 86180 6746.0 16:59:19.734 INFO ProgressMeter - chr17:43093873 13.4 86190 6450.6 16:59:30.527 INFO ProgressMeter - chr17:43095444 13.5 86200 6365.6 16:59:45.685 INFO ProgressMeter - chr17:43104384 13.8 86250 6252.7 16:59:56.058 INFO ProgressMeter - chr17:43125539 14.0 86350 6182.4 17:00:12.905 INFO ProgressMeter - chr17:47425679 14.2 101680 7136.6 17:00:23.409 INFO ProgressMeter - chr17:49624100 14.4 109560 7596.3 17:00:33.990 INFO ProgressMeter - chr17:56369237 14.6 133450 9140.9 17:00:44.877 INFO ProgressMeter - chr17:57983122 14.8 139260 9421.8 17:00:52.775 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.326642936 17:00:52.775 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 572.971809989 17:00:52.776 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 102.80 sec 17:00:52.776 INFO Mutect2 - Shutting down engine [October 8, 2018 5:00:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 15.11 minutes. Runtime.totalMemory()=1594359808 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr17 start:86343962 stop:86344060 contigLength:83257441 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-39/inputs/1547804351/0039-scattered.intervals -O output.vcf Job Mutect2.M2:28:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/tmp.7c6c7712 16:45:12.966 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:13.907 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.907 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:13.907 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:13.907 INFO GetSampleName - Executing as root@19eb1db245f8 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:13.908 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:13.908 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:12 PM UTC 16:45:13.908 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.908 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.909 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:13.909 INFO GetSampleName - Picard Version: 2.18.7 16:45:13.909 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:13.909 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:13.909 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:13.909 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:13.909 INFO GetSampleName - Deflater: IntelDeflater 16:45:13.909 INFO GetSampleName - Inflater: IntelInflater 16:45:13.909 INFO GetSampleName - GCS max retries/reopens: 20 16:45:13.910 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:13.946 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:13.946 INFO GetSampleName - Initializing engine 16:45:20.021 INFO GetSampleName - Done initializing engine 16:45:20.078 INFO ProgressMeter - Starting traversal 16:45:20.079 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:20.083 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:20.083 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:20.083 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:20 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1853882368 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/tmp.7c6c7712 16:45:38.299 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:39.143 INFO GetSampleName - ------------------------------------------------------------ 16:45:39.143 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:39.143 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:39.160 INFO GetSampleName - Executing as root@19eb1db245f8 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:39.160 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:39.160 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:38 PM UTC 16:45:39.160 INFO GetSampleName - ------------------------------------------------------------ 16:45:39.160 INFO GetSampleName - ------------------------------------------------------------ 16:45:39.161 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:39.161 INFO GetSampleName - Picard Version: 2.18.7 16:45:39.161 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:39.161 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:39.169 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:39.169 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:39.169 INFO GetSampleName - Deflater: IntelDeflater 16:45:39.169 INFO GetSampleName - Inflater: IntelInflater 16:45:39.169 INFO GetSampleName - GCS max retries/reopens: 20 16:45:39.170 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:39.171 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:39.171 INFO GetSampleName - Initializing engine 16:45:45.380 INFO GetSampleName - Done initializing engine 16:45:45.440 INFO ProgressMeter - Starting traversal 16:45:45.441 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:45.442 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:45.442 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:45.442 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:45 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1782579200 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/tmp.7c6c7712 16:46:05.401 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:06.738 INFO Mutect2 - ------------------------------------------------------------ 16:46:06.738 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:06.741 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:06.741 INFO Mutect2 - Executing as root@19eb1db245f8 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:06.741 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:06.741 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:05 PM UTC 16:46:06.741 INFO Mutect2 - ------------------------------------------------------------ 16:46:06.741 INFO Mutect2 - ------------------------------------------------------------ 16:46:06.742 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:06.742 INFO Mutect2 - Picard Version: 2.18.7 16:46:06.742 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:06.742 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:06.742 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:06.742 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:06.743 INFO Mutect2 - Deflater: IntelDeflater 16:46:06.743 INFO Mutect2 - Inflater: IntelInflater 16:46:06.743 INFO Mutect2 - GCS max retries/reopens: 20 16:46:06.743 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:06.743 INFO Mutect2 - Initializing engine 16:46:13.330 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:15.663 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:15.902 INFO Mutect2 - Done initializing engine 16:46:16.332 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:16.421 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:16.572 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:16.573 INFO IntelPairHmm - Available threads: 24 16:46:16.573 INFO IntelPairHmm - Requested threads: 4 16:46:16.573 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:17.722 INFO ProgressMeter - Starting traversal 16:46:17.723 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:27.859 INFO ProgressMeter - chr10:126913860 0.2 290 1716.8 16:46:38.015 INFO ProgressMeter - chr10:127050656 0.3 790 2338.9 16:46:48.095 INFO ProgressMeter - chr10:127241178 0.5 1460 2889.8 16:46:58.094 INFO ProgressMeter - chr10:127378640 0.7 1950 2898.1 16:47:02.912 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020157099 16:47:02.912 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 1.1209035680000001 16:47:02.912 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.13 sec 16:47:02.922 INFO Mutect2 - Shutting down engine [October 8, 2018 4:47:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.96 minutes. Runtime.totalMemory()=1960837120 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr10 start:211888755 stop:211888800 contigLength:133797422 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-28/inputs/1547804351/0028-scattered.intervals -O output.vcf Job Mutect2.M2:21:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/tmp.aa340d65 16:45:02.489 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:03.113 INFO GetSampleName - ------------------------------------------------------------ 16:45:03.113 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:03.113 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:03.113 INFO GetSampleName - Executing as root@de574f7ee19e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:03.127 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:03.127 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:02 PM UTC 16:45:03.127 INFO GetSampleName - ------------------------------------------------------------ 16:45:03.127 INFO GetSampleName - ------------------------------------------------------------ 16:45:03.128 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:03.128 INFO GetSampleName - Picard Version: 2.18.7 16:45:03.128 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:03.128 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:03.129 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:03.129 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:03.129 INFO GetSampleName - Deflater: IntelDeflater 16:45:03.129 INFO GetSampleName - Inflater: IntelInflater 16:45:03.129 INFO GetSampleName - GCS max retries/reopens: 20 16:45:03.129 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:03.129 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:03.129 INFO GetSampleName - Initializing engine 16:45:08.859 INFO GetSampleName - Done initializing engine 16:45:08.912 INFO ProgressMeter - Starting traversal 16:45:08.913 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:08.914 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:08.914 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:08.914 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:08 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1701314560 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/tmp.aa340d65 16:45:26.605 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:28.831 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.831 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:28.831 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:28.839 INFO GetSampleName - Executing as root@de574f7ee19e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:28.839 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:28.839 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:26 PM UTC 16:45:28.839 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.839 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.840 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:28.840 INFO GetSampleName - Picard Version: 2.18.7 16:45:28.840 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:28.840 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:28.840 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:28.840 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:28.840 INFO GetSampleName - Deflater: IntelDeflater 16:45:28.840 INFO GetSampleName - Inflater: IntelInflater 16:45:28.841 INFO GetSampleName - GCS max retries/reopens: 20 16:45:28.841 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:28.841 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:28.841 INFO GetSampleName - Initializing engine 16:45:34.181 INFO GetSampleName - Done initializing engine 16:45:34.264 INFO ProgressMeter - Starting traversal 16:45:34.265 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:34.266 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:34.266 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:34.267 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:34 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1699217408 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/tmp.aa340d65 16:45:52.531 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:53.466 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.467 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:53.494 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:53.495 INFO Mutect2 - Executing as root@de574f7ee19e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:53.495 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:53.496 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:52 PM UTC 16:45:53.496 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.496 INFO Mutect2 - ------------------------------------------------------------ 16:45:53.496 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:53.497 INFO Mutect2 - Picard Version: 2.18.7 16:45:53.497 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:53.497 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:53.518 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:53.518 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:53.518 INFO Mutect2 - Deflater: IntelDeflater 16:45:53.519 INFO Mutect2 - Inflater: IntelInflater 16:45:53.519 INFO Mutect2 - GCS max retries/reopens: 20 16:45:53.519 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:53.519 INFO Mutect2 - Initializing engine 16:45:59.759 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:01.943 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:02.195 INFO Mutect2 - Done initializing engine 16:46:02.986 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:03.001 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:03.160 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:03.161 INFO IntelPairHmm - Available threads: 24 16:46:03.161 INFO IntelPairHmm - Requested threads: 4 16:46:03.161 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:04.205 INFO ProgressMeter - Starting traversal 16:46:04.206 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:14.458 INFO ProgressMeter - chr7:119398982 0.2 410 2420.8 16:46:24.410 INFO ProgressMeter - chr7:119620120 0.3 1190 3534.0 16:46:34.542 INFO ProgressMeter - chr7:119867897 0.5 2040 4034.8 16:46:44.698 INFO ProgressMeter - chr7:120040357 0.7 2650 3926.7 16:46:54.780 INFO ProgressMeter - chr7:120404212 0.8 3900 4626.9 16:47:04.788 INFO ProgressMeter - chr7:120819156 1.0 5330 5278.8 16:47:14.924 INFO ProgressMeter - chr7:121225352 1.2 6760 5735.5 16:47:24.936 INFO ProgressMeter - chr7:122113401 1.3 9870 7335.6 16:47:35.010 INFO ProgressMeter - chr7:123591595 1.5 15050 9944.5 16:47:45.023 INFO ProgressMeter - chr7:124865376 1.7 19510 11611.1 16:47:55.026 INFO ProgressMeter - chr7:126029848 1.8 23540 12745.0 16:48:05.034 INFO ProgressMeter - chr7:127122383 2.0 27360 13586.3 16:48:15.036 INFO ProgressMeter - chr7:128595653 2.2 32570 14936.9 16:48:30.685 INFO ProgressMeter - chr7:129127029 2.4 34470 14119.4 16:48:46.057 INFO ProgressMeter - chr7:129129058 2.7 34480 12782.1 16:49:06.034 INFO ProgressMeter - chr7:129207207 3.0 34770 11473.5 16:49:07.160 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.122044963 16:49:07.160 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 35.566538344 16:49:07.162 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 13.67 sec 16:49:07.162 INFO Mutect2 - Shutting down engine [October 8, 2018 4:49:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 3.25 minutes. Runtime.totalMemory()=2081947648 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr7 start:257616765 stop:257616824 contigLength:159345973 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-21/inputs/1547804351/0021-scattered.intervals -O output.vcf Job Mutect2.M2:41:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/tmp.01b0a9a4 16:45:12.235 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:13.067 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.067 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:13.067 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:13.073 INFO GetSampleName - Executing as root@d68ac91befd1 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:13.073 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:13.073 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:11 PM UTC 16:45:13.073 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.073 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.074 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:13.074 INFO GetSampleName - Picard Version: 2.18.7 16:45:13.075 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:13.075 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:13.075 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:13.075 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:13.075 INFO GetSampleName - Deflater: IntelDeflater 16:45:13.075 INFO GetSampleName - Inflater: IntelInflater 16:45:13.075 INFO GetSampleName - GCS max retries/reopens: 20 16:45:13.075 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:13.076 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:13.076 INFO GetSampleName - Initializing engine 16:45:20.377 INFO GetSampleName - Done initializing engine 16:45:20.436 INFO ProgressMeter - Starting traversal 16:45:20.439 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:20.440 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:20.444 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:20.444 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:20 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=1795686400 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/tmp.01b0a9a4 16:45:37.937 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:38.713 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.713 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:38.713 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:38.730 INFO GetSampleName - Executing as root@d68ac91befd1 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:38.730 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:38.731 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:37 PM UTC 16:45:38.731 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.731 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.731 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:38.732 INFO GetSampleName - Picard Version: 2.18.7 16:45:38.732 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:38.732 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:38.732 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:38.732 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:38.732 INFO GetSampleName - Deflater: IntelDeflater 16:45:38.732 INFO GetSampleName - Inflater: IntelInflater 16:45:38.732 INFO GetSampleName - GCS max retries/reopens: 20 16:45:38.732 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:38.733 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:38.753 INFO GetSampleName - Initializing engine 16:45:44.431 INFO GetSampleName - Done initializing engine 16:45:44.488 INFO ProgressMeter - Starting traversal 16:45:44.489 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:44.490 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:44.490 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:44.490 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:44 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1739587584 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/tmp.01b0a9a4 16:46:02.677 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:03.694 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.694 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:03.694 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:03.694 INFO Mutect2 - Executing as root@d68ac91befd1 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:03.695 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:03.706 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:02 PM UTC 16:46:03.706 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.706 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.707 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:03.707 INFO Mutect2 - Picard Version: 2.18.7 16:46:03.707 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:03.707 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:03.707 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:03.707 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:03.707 INFO Mutect2 - Deflater: IntelDeflater 16:46:03.707 INFO Mutect2 - Inflater: IntelInflater 16:46:03.707 INFO Mutect2 - GCS max retries/reopens: 20 16:46:03.707 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:03.707 INFO Mutect2 - Initializing engine 16:46:10.216 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:12.361 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:12.596 INFO Mutect2 - Done initializing engine 16:46:13.006 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:13.022 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:13.219 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:13.220 INFO IntelPairHmm - Available threads: 24 16:46:13.220 INFO IntelPairHmm - Requested threads: 4 16:46:13.220 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:14.885 INFO ProgressMeter - Starting traversal 16:46:14.885 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:25.048 INFO ProgressMeter - chr18:64263197 0.2 270 1599.7 16:46:35.224 INFO ProgressMeter - chr18:64498459 0.3 1100 3245.0 16:46:45.230 INFO ProgressMeter - chr18:64701319 0.5 1820 3598.6 16:46:55.238 INFO ProgressMeter - chr18:64976854 0.7 2790 4148.5 16:47:05.255 INFO ProgressMeter - chr18:65288916 0.8 3880 4621.8 16:47:15.452 INFO ProgressMeter - chr18:65801754 1.0 5660 5607.0 16:47:25.788 INFO ProgressMeter - chr18:66542944 1.2 8250 6981.4 16:47:35.799 INFO ProgressMeter - chr18:68612877 1.3 15370 11397.3 16:47:45.870 INFO ProgressMeter - chr18:70893442 1.5 23210 15305.8 16:47:55.880 INFO ProgressMeter - chr18:72179226 1.7 27650 16426.6 16:48:04.868 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.05339863500000001 16:48:04.868 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 5.966706835 16:48:04.868 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 3.19 sec 16:48:04.869 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.04 minutes. Runtime.totalMemory()=2123366400 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr18 start:91128297 stop:91128342 contigLength:80373285 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-41/inputs/1547804351/0041-scattered.intervals -O output.vcf Job Mutect2.M2:25:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/tmp.4faa1823 16:45:08.169 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:08.823 INFO GetSampleName - ------------------------------------------------------------ 16:45:08.824 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:08.824 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:08.824 INFO GetSampleName - Executing as root@2f30375fc10c on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:08.824 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:08.824 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:08 PM UTC 16:45:08.824 INFO GetSampleName - ------------------------------------------------------------ 16:45:08.824 INFO GetSampleName - ------------------------------------------------------------ 16:45:08.841 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:08.841 INFO GetSampleName - Picard Version: 2.18.7 16:45:08.841 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:08.842 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:08.842 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:08.842 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:08.842 INFO GetSampleName - Deflater: IntelDeflater 16:45:08.842 INFO GetSampleName - Inflater: IntelInflater 16:45:08.842 INFO GetSampleName - GCS max retries/reopens: 20 16:45:08.842 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:08.842 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:08.842 INFO GetSampleName - Initializing engine 16:45:14.631 INFO GetSampleName - Done initializing engine 16:45:14.681 INFO ProgressMeter - Starting traversal 16:45:14.683 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:14.684 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:14.684 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:14.684 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:14 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1741684736 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/tmp.4faa1823 16:45:31.998 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:32.864 INFO GetSampleName - ------------------------------------------------------------ 16:45:32.864 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:32.864 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:32.868 INFO GetSampleName - Executing as root@2f30375fc10c on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:32.869 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:32.869 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:31 PM UTC 16:45:32.869 INFO GetSampleName - ------------------------------------------------------------ 16:45:32.869 INFO GetSampleName - ------------------------------------------------------------ 16:45:32.870 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:32.870 INFO GetSampleName - Picard Version: 2.18.7 16:45:32.870 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:32.870 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:32.870 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:32.870 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:32.870 INFO GetSampleName - Deflater: IntelDeflater 16:45:32.870 INFO GetSampleName - Inflater: IntelInflater 16:45:32.870 INFO GetSampleName - GCS max retries/reopens: 20 16:45:32.870 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:32.871 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:32.871 INFO GetSampleName - Initializing engine 16:45:38.672 INFO GetSampleName - Done initializing engine 16:45:38.727 INFO ProgressMeter - Starting traversal 16:45:38.729 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:38.730 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:38.730 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:38.730 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:38 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1810366464 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/tmp.4faa1823 16:45:57.424 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:58.435 INFO Mutect2 - ------------------------------------------------------------ 16:45:58.435 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:58.435 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:58.439 INFO Mutect2 - Executing as root@2f30375fc10c on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:58.439 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:58.440 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:57 PM UTC 16:45:58.440 INFO Mutect2 - ------------------------------------------------------------ 16:45:58.440 INFO Mutect2 - ------------------------------------------------------------ 16:45:58.440 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:58.440 INFO Mutect2 - Picard Version: 2.18.7 16:45:58.440 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:58.441 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:58.441 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:58.441 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:58.441 INFO Mutect2 - Deflater: IntelDeflater 16:45:58.441 INFO Mutect2 - Inflater: IntelInflater 16:45:58.441 INFO Mutect2 - GCS max retries/reopens: 20 16:45:58.441 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:58.441 INFO Mutect2 - Initializing engine 16:46:05.492 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:07.567 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:07.896 INFO Mutect2 - Done initializing engine 16:46:08.226 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:08.267 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:08.417 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:08.417 INFO IntelPairHmm - Available threads: 24 16:46:08.417 INFO IntelPairHmm - Requested threads: 4 16:46:08.418 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:09.550 INFO ProgressMeter - Starting traversal 16:46:09.550 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:19.910 INFO ProgressMeter - chr9:72281602 0.2 340 1969.3 16:46:30.081 INFO ProgressMeter - chr9:72666495 0.3 1670 4888.0 16:46:40.090 INFO ProgressMeter - chr9:72907524 0.5 2510 4936.7 16:46:50.138 INFO ProgressMeter - chr9:73280062 0.7 3790 5602.8 16:47:00.143 INFO ProgressMeter - chr9:73634238 0.8 5010 5941.5 16:47:10.447 INFO ProgressMeter - chr9:74060798 1.0 6470 6374.7 16:47:20.534 INFO ProgressMeter - chr9:74710390 1.2 8690 7345.3 16:47:27.395 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00384504 16:47:27.395 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 2.349971054 16:47:27.395 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.81 sec 16:47:27.399 INFO Mutect2 - Shutting down engine [October 8, 2018 4:47:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 1.50 minutes. Runtime.totalMemory()=1986002944 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr9 start:145842401 stop:145842474 contigLength:138394717 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-25/inputs/1547804351/0025-scattered.intervals -O output.vcf Job Mutect2.M2:2:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/tmp.914dd572 16:45:03.958 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:04.803 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.803 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:04.803 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:04.803 INFO GetSampleName - Executing as root@2d2a55432e1a on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:04.804 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:04.804 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:03 PM UTC 16:45:04.804 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.804 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.804 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:04.805 INFO GetSampleName - Picard Version: 2.18.7 16:45:04.811 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:04.811 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:04.811 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:04.811 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:04.811 INFO GetSampleName - Deflater: IntelDeflater 16:45:04.811 INFO GetSampleName - Inflater: IntelInflater 16:45:04.811 INFO GetSampleName - GCS max retries/reopens: 20 16:45:04.811 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:04.812 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:04.812 INFO GetSampleName - Initializing engine 16:45:10.674 INFO GetSampleName - Done initializing engine 16:45:10.721 INFO ProgressMeter - Starting traversal 16:45:10.722 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:10.723 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:10.725 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:10.725 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:10 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1725431808 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/tmp.914dd572 16:45:29.166 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:29.892 INFO GetSampleName - ------------------------------------------------------------ 16:45:29.893 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:29.893 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:29.893 INFO GetSampleName - Executing as root@2d2a55432e1a on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:29.893 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:29.894 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:29 PM UTC 16:45:29.894 INFO GetSampleName - ------------------------------------------------------------ 16:45:29.894 INFO GetSampleName - ------------------------------------------------------------ 16:45:29.894 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:29.894 INFO GetSampleName - Picard Version: 2.18.7 16:45:29.894 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:29.894 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:29.895 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:29.895 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:29.895 INFO GetSampleName - Deflater: IntelDeflater 16:45:29.895 INFO GetSampleName - Inflater: IntelInflater 16:45:29.895 INFO GetSampleName - GCS max retries/reopens: 20 16:45:29.895 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:29.895 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:29.895 INFO GetSampleName - Initializing engine 16:45:36.100 INFO GetSampleName - Done initializing engine 16:45:36.161 INFO ProgressMeter - Starting traversal 16:45:36.162 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:36.163 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:36.163 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:36.163 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:36 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1745879040 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/tmp.914dd572 16:45:54.897 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:55.966 INFO Mutect2 - ------------------------------------------------------------ 16:45:55.967 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:55.967 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:55.967 INFO Mutect2 - Executing as root@2d2a55432e1a on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:55.967 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:55.967 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:54 PM UTC 16:45:55.967 INFO Mutect2 - ------------------------------------------------------------ 16:45:55.968 INFO Mutect2 - ------------------------------------------------------------ 16:45:55.968 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:55.968 INFO Mutect2 - Picard Version: 2.18.7 16:45:55.968 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:55.968 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:55.968 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:55.968 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:55.969 INFO Mutect2 - Deflater: IntelDeflater 16:45:55.969 INFO Mutect2 - Inflater: IntelInflater 16:45:55.969 INFO Mutect2 - GCS max retries/reopens: 20 16:45:55.969 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:55.969 INFO Mutect2 - Initializing engine 16:46:02.818 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:05.093 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:05.329 INFO Mutect2 - Done initializing engine 16:46:05.754 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:05.867 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:06.126 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:06.127 INFO IntelPairHmm - Available threads: 24 16:46:06.127 INFO IntelPairHmm - Requested threads: 4 16:46:06.127 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:07.505 INFO ProgressMeter - Starting traversal 16:46:07.505 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:17.508 INFO ProgressMeter - chr1:133982577 0.2 17630 105780.0 16:46:32.877 INFO ProgressMeter - chr1:143185600 0.4 48310 114248.6 16:46:43.108 INFO ProgressMeter - chr1:143203510 0.6 48390 81549.3 16:46:53.956 INFO ProgressMeter - chr1:143216536 0.8 48460 62597.7 16:47:04.247 INFO ProgressMeter - chr1:143227729 0.9 48520 51372.9 16:47:16.236 INFO ProgressMeter - chr1:143248760 1.1 48610 42435.6 16:47:36.686 INFO ProgressMeter - chr1:143264859 1.5 48690 32758.1 16:47:47.611 INFO ProgressMeter - chr1:143464826 1.7 49390 29602.6 16:47:57.622 INFO ProgressMeter - chr1:144444999 1.8 52720 28725.8 16:48:07.649 INFO ProgressMeter - chr1:146773904 2.0 60680 30303.6 16:48:17.821 INFO ProgressMeter - chr1:149883256 2.2 71340 32846.6 16:48:27.869 INFO ProgressMeter - chr1:150901841 2.3 75020 32068.1 16:48:38.025 INFO ProgressMeter - chr1:152532475 2.5 80890 32244.2 16:48:48.049 INFO ProgressMeter - chr1:154326761 2.7 87330 32637.8 16:48:57.558 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037794543 16:48:57.558 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 19.810507943 16:48:57.559 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 27.97 sec 16:48:57.560 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 3.05 minutes. Runtime.totalMemory()=2215116800 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr1 start:271283985 stop:271284040 contigLength:248956422 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-2/inputs/1547804351/0002-scattered.intervals -O output.vcf Job Mutect2.M2:49:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/tmp.39c2731c 16:45:01.813 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:02.715 INFO GetSampleName - ------------------------------------------------------------ 16:45:02.715 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:02.715 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:02.716 INFO GetSampleName - Executing as root@a6913af7177c on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:02.716 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:02.716 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:01 PM UTC 16:45:02.716 INFO GetSampleName - ------------------------------------------------------------ 16:45:02.716 INFO GetSampleName - ------------------------------------------------------------ 16:45:02.717 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:02.717 INFO GetSampleName - Picard Version: 2.18.7 16:45:02.717 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:02.717 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:02.717 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:02.717 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:02.717 INFO GetSampleName - Deflater: IntelDeflater 16:45:02.717 INFO GetSampleName - Inflater: IntelInflater 16:45:02.717 INFO GetSampleName - GCS max retries/reopens: 20 16:45:02.717 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:02.736 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:02.736 INFO GetSampleName - Initializing engine 16:45:08.717 INFO GetSampleName - Done initializing engine 16:45:08.773 INFO ProgressMeter - Starting traversal 16:45:08.774 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:08.775 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:08.775 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:08.775 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:08 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1787297792 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/tmp.39c2731c 16:45:25.003 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:27.183 INFO GetSampleName - ------------------------------------------------------------ 16:45:27.183 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:27.183 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:27.204 INFO GetSampleName - Executing as root@a6913af7177c on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:27.204 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:27.204 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:24 PM UTC 16:45:27.204 INFO GetSampleName - ------------------------------------------------------------ 16:45:27.204 INFO GetSampleName - ------------------------------------------------------------ 16:45:27.205 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:27.205 INFO GetSampleName - Picard Version: 2.18.7 16:45:27.205 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:27.205 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:27.216 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:27.216 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:27.216 INFO GetSampleName - Deflater: IntelDeflater 16:45:27.216 INFO GetSampleName - Inflater: IntelInflater 16:45:27.216 INFO GetSampleName - GCS max retries/reopens: 20 16:45:27.216 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:27.217 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:27.217 INFO GetSampleName - Initializing engine 16:45:32.936 INFO GetSampleName - Done initializing engine 16:45:33.035 INFO ProgressMeter - Starting traversal 16:45:33.035 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:33.037 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:33.037 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:33.037 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:33 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=1773142016 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/tmp.39c2731c 16:45:51.370 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:52.485 INFO Mutect2 - ------------------------------------------------------------ 16:45:52.485 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:52.486 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:52.487 INFO Mutect2 - Executing as root@a6913af7177c on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:52.506 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:52.506 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:51 PM UTC 16:45:52.506 INFO Mutect2 - ------------------------------------------------------------ 16:45:52.506 INFO Mutect2 - ------------------------------------------------------------ 16:45:52.509 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:52.509 INFO Mutect2 - Picard Version: 2.18.7 16:45:52.510 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:52.510 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:52.525 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:52.525 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:52.525 INFO Mutect2 - Deflater: IntelDeflater 16:45:52.526 INFO Mutect2 - Inflater: IntelInflater 16:45:52.526 INFO Mutect2 - GCS max retries/reopens: 20 16:45:52.526 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:52.526 INFO Mutect2 - Initializing engine 16:45:58.699 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:01.489 INFO IntervalArgumentCollection - Processing 64346955 bp from intervals 16:46:02.876 INFO Mutect2 - Done initializing engine 16:46:03.615 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:03.646 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:03.838 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:03.839 INFO IntelPairHmm - Available threads: 24 16:46:03.839 INFO IntelPairHmm - Requested threads: 4 16:46:03.839 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:05.105 INFO ProgressMeter - Starting traversal 16:46:05.106 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:15.130 INFO ProgressMeter - chr22_GL383582v2_alt:131449 0.2 1790 10715.4 16:46:25.835 INFO ProgressMeter - chr2_KI270894v1_alt:2101 0.3 10020 29002.8 16:46:35.920 INFO ProgressMeter - chr4_KI270896v1_alt:1801 0.5 11830 23035.0 16:46:45.924 INFO ProgressMeter - chr6_GL000251v2_alt:485101 0.7 18960 27870.1 16:46:55.942 INFO ProgressMeter - chr6_GL000251v2_alt:1648625 0.8 22840 26957.3 16:47:06.007 INFO ProgressMeter - chr6_GL000251v2_alt:3004148 1.0 27360 26955.2 16:47:16.020 INFO ProgressMeter - chr7_KI270899v1_alt:64501 1.2 33550 28386.5 16:47:26.547 INFO ProgressMeter - chr15_KI270905v1_alt:2701 1.4 39140 28836.0 16:47:36.559 INFO ProgressMeter - chr15_KI270905v1_alt:4423597 1.5 53900 35363.2 16:47:46.560 INFO ProgressMeter - chr19_KI270921v1_alt:105901 1.7 72680 42983.0 16:47:56.560 INFO ProgressMeter - chr19_KI270931v1_alt:9901 1.9 99250 53430.1 16:47:59.638 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.022299615000000002 16:47:59.638 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.309085902 16:47:59.638 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.25 sec 16:47:59.639 INFO Mutect2 - Shutting down engine [October 8, 2018 4:47:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.14 minutes. Runtime.totalMemory()=2134900736 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr6_GL000253v2_alt start:62876595 stop:62876616 contigLength:4677643 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-49/inputs/1547804351/0049-scattered.intervals -O output.vcf Job Mutect2.M2:47:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/tmp.cfd03206 16:44:58.813 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:44:59.604 INFO GetSampleName - ------------------------------------------------------------ 16:44:59.604 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:44:59.604 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:44:59.605 INFO GetSampleName - Executing as root@dfeab283189e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:44:59.605 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:44:59.605 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:58 PM UTC 16:44:59.605 INFO GetSampleName - ------------------------------------------------------------ 16:44:59.605 INFO GetSampleName - ------------------------------------------------------------ 16:44:59.624 INFO GetSampleName - HTSJDK Version: 2.16.0 16:44:59.624 INFO GetSampleName - Picard Version: 2.18.7 16:44:59.624 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:44:59.624 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:44:59.625 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:44:59.625 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:44:59.625 INFO GetSampleName - Deflater: IntelDeflater 16:44:59.625 INFO GetSampleName - Inflater: IntelInflater 16:44:59.625 INFO GetSampleName - GCS max retries/reopens: 20 16:44:59.625 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:44:59.639 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:44:59.639 INFO GetSampleName - Initializing engine 16:45:05.194 INFO GetSampleName - Done initializing engine 16:45:05.251 INFO ProgressMeter - Starting traversal 16:45:05.253 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:05.254 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:05.254 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:05.254 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:05 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1741160448 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/tmp.cfd03206 16:45:22.830 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:23.986 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.987 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:23.987 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:23.987 INFO GetSampleName - Executing as root@dfeab283189e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:23.987 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:23.987 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:22 PM UTC 16:45:23.987 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.987 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.988 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:23.988 INFO GetSampleName - Picard Version: 2.18.7 16:45:23.988 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:23.988 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:23.988 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:23.988 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:23.988 INFO GetSampleName - Deflater: IntelDeflater 16:45:23.989 INFO GetSampleName - Inflater: IntelInflater 16:45:23.989 INFO GetSampleName - GCS max retries/reopens: 20 16:45:23.989 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:23.989 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:23.989 INFO GetSampleName - Initializing engine 16:45:29.953 INFO GetSampleName - Done initializing engine 16:45:30.040 INFO ProgressMeter - Starting traversal 16:45:30.042 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:30.043 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:30.043 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:30.043 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:30 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1778384896 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/tmp.cfd03206 16:45:48.675 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:49.849 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.850 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:49.850 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:49.851 INFO Mutect2 - Executing as root@dfeab283189e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:49.852 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:49.852 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:48 PM UTC 16:45:49.852 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.852 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.852 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:49.853 INFO Mutect2 - Picard Version: 2.18.7 16:45:49.853 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:49.853 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:49.853 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:49.853 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:49.853 INFO Mutect2 - Deflater: IntelDeflater 16:45:49.853 INFO Mutect2 - Inflater: IntelInflater 16:45:49.853 INFO Mutect2 - GCS max retries/reopens: 20 16:45:49.853 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:49.854 INFO Mutect2 - Initializing engine 16:45:56.370 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:58.627 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:59.059 INFO Mutect2 - Done initializing engine 16:45:59.926 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:45:59.934 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:00.150 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:00.151 INFO IntelPairHmm - Available threads: 24 16:46:00.151 INFO IntelPairHmm - Requested threads: 4 16:46:00.151 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:01.918 INFO ProgressMeter - Starting traversal 16:46:01.918 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:11.939 INFO ProgressMeter - chrX:149401959 0.2 330 1976.2 16:46:22.023 INFO ProgressMeter - chrX:149762742 0.3 1550 4626.2 16:46:32.103 INFO ProgressMeter - chrX:150436663 0.5 3840 7633.2 16:46:42.199 INFO ProgressMeter - chrX:150996547 0.7 5750 8565.0 16:46:52.333 INFO ProgressMeter - chrX:151531220 0.8 7560 8997.5 16:47:02.688 INFO ProgressMeter - chrX:152005530 1.0 9180 9064.4 16:47:12.757 INFO ProgressMeter - chrX:152633129 1.2 11330 9596.5 16:47:22.874 INFO ProgressMeter - chrX:153470166 1.3 14180 10509.5 16:47:29.964 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.035661803 16:47:29.964 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 2.2084894150000003 16:47:29.964 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.20 sec 16:47:29.967 INFO Mutect2 - Shutting down engine [October 8, 2018 4:47:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 1.69 minutes. Runtime.totalMemory()=1946157056 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chrX start:181792155 stop:181792237 contigLength:156040895 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-47/inputs/1547804351/0047-scattered.intervals -O output.vcf Job Mutect2.M2:3:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/tmp.aca7b435 16:45:11.013 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:11.757 INFO GetSampleName - ------------------------------------------------------------ 16:45:11.771 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:11.771 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:11.772 INFO GetSampleName - Executing as root@05a96f318dbb on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:11.772 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:11.772 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:10 PM UTC 16:45:11.772 INFO GetSampleName - ------------------------------------------------------------ 16:45:11.772 INFO GetSampleName - ------------------------------------------------------------ 16:45:11.773 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:11.773 INFO GetSampleName - Picard Version: 2.18.7 16:45:11.773 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:11.773 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:11.773 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:11.773 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:11.773 INFO GetSampleName - Deflater: IntelDeflater 16:45:11.773 INFO GetSampleName - Inflater: IntelInflater 16:45:11.773 INFO GetSampleName - GCS max retries/reopens: 20 16:45:11.773 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:11.804 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:11.804 INFO GetSampleName - Initializing engine 16:45:18.342 INFO GetSampleName - Done initializing engine 16:45:18.401 INFO ProgressMeter - Starting traversal 16:45:18.402 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:18.418 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:18.432 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:18.432 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1759510528 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/tmp.aca7b435 16:45:36.552 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:37.519 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.519 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:37.520 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:37.520 INFO GetSampleName - Executing as root@05a96f318dbb on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:37.520 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:37.520 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:36 PM UTC 16:45:37.520 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.520 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.521 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:37.521 INFO GetSampleName - Picard Version: 2.18.7 16:45:37.521 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:37.521 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:37.521 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:37.522 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:37.522 INFO GetSampleName - Deflater: IntelDeflater 16:45:37.522 INFO GetSampleName - Inflater: IntelInflater 16:45:37.522 INFO GetSampleName - GCS max retries/reopens: 20 16:45:37.522 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:37.522 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:37.522 INFO GetSampleName - Initializing engine 16:45:44.016 INFO GetSampleName - Done initializing engine 16:45:44.115 INFO ProgressMeter - Starting traversal 16:45:44.117 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:44.118 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:44.119 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:44.119 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:44 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1799880704 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/tmp.aca7b435 16:46:02.802 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:03.956 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.956 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:03.957 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:03.959 INFO Mutect2 - Executing as root@05a96f318dbb on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:03.959 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:03.960 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:02 PM UTC 16:46:03.960 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.960 INFO Mutect2 - ------------------------------------------------------------ 16:46:03.960 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:03.960 INFO Mutect2 - Picard Version: 2.18.7 16:46:03.961 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:03.961 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:03.961 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:03.961 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:03.961 INFO Mutect2 - Deflater: IntelDeflater 16:46:03.961 INFO Mutect2 - Inflater: IntelInflater 16:46:03.961 INFO Mutect2 - GCS max retries/reopens: 20 16:46:03.961 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:03.962 INFO Mutect2 - Initializing engine 16:46:11.367 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:14.092 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:14.464 INFO Mutect2 - Done initializing engine 16:46:14.837 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:14.857 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:15.021 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:15.022 INFO IntelPairHmm - Available threads: 24 16:46:15.022 INFO IntelPairHmm - Requested threads: 4 16:46:15.023 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:16.242 INFO ProgressMeter - Starting traversal 16:46:16.242 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:31.870 INFO ProgressMeter - chr1:193122159 0.3 290 1114.0 16:46:45.316 INFO ProgressMeter - chr1:193125046 0.5 300 619.1 16:47:43.766 INFO ProgressMeter - chr1:193135882 1.5 350 239.9 16:48:04.038 INFO ProgressMeter - chr1:193139656 1.8 370 205.9 16:48:14.443 INFO ProgressMeter - chr1:193142145 2.0 380 192.9 16:48:17.586 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.136197219 16:48:17.586 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 51.527632003 16:48:17.586 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 20.89 sec 16:48:17.587 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.25 minutes. Runtime.totalMemory()=1967652864 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr1 start:344028725 stop:344028776 contigLength:248956422 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-3/inputs/1547804351/0003-scattered.intervals -O output.vcf Job Mutect2.M2:20:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/tmp.959948aa 16:45:03.301 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:04.127 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.128 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:04.128 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:04.128 INFO GetSampleName - Executing as root@004f67a67b54 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:04.128 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:04.129 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:03 PM UTC 16:45:04.129 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.129 INFO GetSampleName - ------------------------------------------------------------ 16:45:04.129 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:04.129 INFO GetSampleName - Picard Version: 2.18.7 16:45:04.129 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:04.129 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:04.130 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:04.130 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:04.130 INFO GetSampleName - Deflater: IntelDeflater 16:45:04.130 INFO GetSampleName - Inflater: IntelInflater 16:45:04.130 INFO GetSampleName - GCS max retries/reopens: 20 16:45:04.130 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:04.130 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:04.130 INFO GetSampleName - Initializing engine 16:45:10.308 INFO GetSampleName - Done initializing engine 16:45:10.355 INFO ProgressMeter - Starting traversal 16:45:10.356 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:10.358 INFO ProgressMeter - unmapped 0.0 0 0.0 16:45:10.358 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:10.358 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:10 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1792540672 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/tmp.959948aa 16:45:29.580 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:30.623 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.625 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:30.626 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:30.630 INFO GetSampleName - Executing as root@004f67a67b54 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:30.631 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:30.631 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:29 PM UTC 16:45:30.631 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.631 INFO GetSampleName - ------------------------------------------------------------ 16:45:30.632 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:30.632 INFO GetSampleName - Picard Version: 2.18.7 16:45:30.632 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:30.632 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:30.632 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:30.632 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:30.632 INFO GetSampleName - Deflater: IntelDeflater 16:45:30.632 INFO GetSampleName - Inflater: IntelInflater 16:45:30.632 INFO GetSampleName - GCS max retries/reopens: 20 16:45:30.632 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:30.633 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:30.633 INFO GetSampleName - Initializing engine 16:45:36.949 INFO GetSampleName - Done initializing engine 16:45:37.005 INFO ProgressMeter - Starting traversal 16:45:37.006 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:37.007 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:37.007 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:37.007 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:37 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1801977856 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/tmp.959948aa 16:45:55.508 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:56.543 INFO Mutect2 - ------------------------------------------------------------ 16:45:56.543 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:56.561 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:56.562 INFO Mutect2 - Executing as root@004f67a67b54 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:56.573 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:56.573 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:55 PM UTC 16:45:56.573 INFO Mutect2 - ------------------------------------------------------------ 16:45:56.573 INFO Mutect2 - ------------------------------------------------------------ 16:45:56.574 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:56.574 INFO Mutect2 - Picard Version: 2.18.7 16:45:56.574 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:56.574 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:56.597 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:56.597 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:56.597 INFO Mutect2 - Deflater: IntelDeflater 16:45:56.597 INFO Mutect2 - Inflater: IntelInflater 16:45:56.597 INFO Mutect2 - GCS max retries/reopens: 20 16:45:56.597 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:56.598 INFO Mutect2 - Initializing engine 16:46:03.908 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:05.947 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:06.230 INFO Mutect2 - Done initializing engine 16:46:06.652 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:06.661 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:06.841 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:06.842 INFO IntelPairHmm - Available threads: 24 16:46:06.842 INFO IntelPairHmm - Requested threads: 4 16:46:06.842 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:08.027 INFO ProgressMeter - Starting traversal 16:46:08.028 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:18.270 INFO ProgressMeter - chr7:54974268 0.2 140 820.2 16:47:07.031 INFO ProgressMeter - chr7:55142568 1.0 730 742.3 16:47:42.881 INFO ProgressMeter - chr7:55145085 1.6 740 468.1 16:48:16.787 INFO ProgressMeter - chr7:55152444 2.1 770 358.8 16:49:00.198 INFO ProgressMeter - chr7:55156899 2.9 790 275.3 16:49:13.045 INFO ProgressMeter - chr7:55157822 3.1 800 259.4 16:49:34.082 INFO ProgressMeter - chr7:55161867 3.4 820 238.8 16:50:15.061 INFO ProgressMeter - chr7:55170369 4.1 860 208.9 16:50:34.167 INFO ProgressMeter - chr7:55174613 4.4 880 198.4 16:50:55.697 INFO ProgressMeter - chr7:55176576 4.8 890 185.6 16:51:14.680 INFO ProgressMeter - chr7:55193887 5.1 970 189.8 16:51:43.162 INFO ProgressMeter - chr7:55201859 5.6 1010 180.8 16:51:58.832 INFO ProgressMeter - chr7:55206054 5.8 1030 176.2 16:52:08.861 INFO ProgressMeter - chr7:56364895 6.0 5160 858.0 16:52:21.497 INFO ProgressMeter - chr7:57611936 6.2 9520 1529.4 16:52:31.502 INFO ProgressMeter - chr7:63995620 6.4 31370 4908.3 16:52:41.518 INFO ProgressMeter - chr7:67050587 6.6 42180 6431.7 16:52:51.521 INFO ProgressMeter - chr7:69330717 6.7 50250 7472.3 16:53:01.523 INFO ProgressMeter - chr7:73524279 6.9 65030 9436.1 16:53:11.544 INFO ProgressMeter - chr7:77392661 7.1 78750 11156.6 16:53:21.564 INFO ProgressMeter - chr7:81267787 7.2 92390 12786.5 16:53:35.007 INFO ProgressMeter - chr7:81704762 7.4 93960 12612.7 16:53:54.215 INFO ProgressMeter - chr7:81706868 7.8 93970 12094.3 16:54:04.554 INFO ProgressMeter - chr7:81710792 7.9 93990 11834.4 16:54:21.358 INFO ProgressMeter - chr7:81744475 8.2 94120 11447.1 16:54:32.930 INFO ProgressMeter - chr7:81757039 8.4 94180 11191.9 16:54:47.908 INFO ProgressMeter - chr7:81763107 8.7 94210 10872.9 16:54:57.918 INFO ProgressMeter - chr7:85678443 8.8 108030 12232.4 16:55:07.922 INFO ProgressMeter - chr7:89382927 9.0 121190 13468.2 16:55:20.182 INFO ProgressMeter - chr7:92727068 9.2 133130 14466.6 16:55:32.306 INFO ProgressMeter - chr7:96284155 9.4 145570 15478.5 16:55:42.306 INFO ProgressMeter - chr7:100609746 9.6 160960 16816.9 16:55:52.306 INFO ProgressMeter - chr7:105454886 9.7 178120 18291.3 16:55:53.737 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.257679437 16:55:53.737 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 338.58229375900004 16:55:53.737 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 70.70 sec 16:55:53.738 INFO Mutect2 - Shutting down engine [October 8, 2018 4:55:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 9.97 minutes. Runtime.totalMemory()=2160590848 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr7 start:171907831 stop:171907910 contigLength:159345973 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-20/inputs/1547804351/0020-scattered.intervals -O output.vcf Job Mutect2.M2:10:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/tmp.844f2177 16:45:04.250 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:05.072 INFO GetSampleName - ------------------------------------------------------------ 16:45:05.072 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:05.072 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:05.076 INFO GetSampleName - Executing as root@b3bccb49d624 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:05.076 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:05.076 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:04 PM UTC 16:45:05.076 INFO GetSampleName - ------------------------------------------------------------ 16:45:05.077 INFO GetSampleName - ------------------------------------------------------------ 16:45:05.077 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:05.077 INFO GetSampleName - Picard Version: 2.18.7 16:45:05.077 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:05.078 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:05.078 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:05.078 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:05.078 INFO GetSampleName - Deflater: IntelDeflater 16:45:05.078 INFO GetSampleName - Inflater: IntelInflater 16:45:05.078 INFO GetSampleName - GCS max retries/reopens: 20 16:45:05.078 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:05.078 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:05.078 INFO GetSampleName - Initializing engine 16:45:10.898 INFO GetSampleName - Done initializing engine 16:45:10.948 INFO ProgressMeter - Starting traversal 16:45:10.949 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:10.962 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:10.962 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:10.962 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:10 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1795686400 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/tmp.844f2177 16:45:27.363 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:28.373 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.373 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:28.373 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:28.374 INFO GetSampleName - Executing as root@b3bccb49d624 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:28.374 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:28.374 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:27 PM UTC 16:45:28.374 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.374 INFO GetSampleName - ------------------------------------------------------------ 16:45:28.375 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:28.375 INFO GetSampleName - Picard Version: 2.18.7 16:45:28.375 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:28.375 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:28.375 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:28.375 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:28.391 INFO GetSampleName - Deflater: IntelDeflater 16:45:28.391 INFO GetSampleName - Inflater: IntelInflater 16:45:28.391 INFO GetSampleName - GCS max retries/reopens: 20 16:45:28.391 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:28.391 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:28.392 INFO GetSampleName - Initializing engine 16:45:33.861 INFO GetSampleName - Done initializing engine 16:45:33.916 INFO ProgressMeter - Starting traversal 16:45:33.917 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:33.918 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:33.918 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:33.918 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:33 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1750597632 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/tmp.844f2177 16:45:52.970 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:54.046 INFO Mutect2 - ------------------------------------------------------------ 16:45:54.046 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:54.046 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:54.047 INFO Mutect2 - Executing as root@b3bccb49d624 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:54.047 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:54.047 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:52 PM UTC 16:45:54.047 INFO Mutect2 - ------------------------------------------------------------ 16:45:54.047 INFO Mutect2 - ------------------------------------------------------------ 16:45:54.083 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:54.083 INFO Mutect2 - Picard Version: 2.18.7 16:45:54.083 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:54.083 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:54.083 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:54.084 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:54.084 INFO Mutect2 - Deflater: IntelDeflater 16:45:54.084 INFO Mutect2 - Inflater: IntelInflater 16:45:54.084 INFO Mutect2 - GCS max retries/reopens: 20 16:45:54.084 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:54.084 INFO Mutect2 - Initializing engine 16:46:00.529 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:02.521 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:02.737 INFO Mutect2 - Done initializing engine 16:46:03.042 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:03.051 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:03.264 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:03.264 INFO IntelPairHmm - Available threads: 24 16:46:03.264 INFO IntelPairHmm - Requested threads: 4 16:46:03.265 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:04.350 INFO ProgressMeter - Starting traversal 16:46:04.350 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:14.473 INFO ProgressMeter - chr3:152385534 0.2 230 1363.4 16:46:24.641 INFO ProgressMeter - chr3:152637721 0.3 1120 3311.8 16:46:34.961 INFO ProgressMeter - chr3:152810413 0.5 1740 3410.5 16:46:45.147 INFO ProgressMeter - chr3:152965644 0.7 2290 3368.0 16:46:55.341 INFO ProgressMeter - chr3:153198662 0.8 3140 3694.8 16:47:05.371 INFO ProgressMeter - chr3:153557784 1.0 4400 4326.5 16:47:39.328 INFO ProgressMeter - chr3:154025298 1.6 6070 3834.6 16:47:49.328 INFO ProgressMeter - chr3:155076236 1.7 9790 5595.5 16:47:59.344 INFO ProgressMeter - chr3:156160824 1.9 13640 7116.9 16:48:09.346 INFO ProgressMeter - chr3:157931248 2.1 19900 9552.3 16:48:19.062 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.077737741 16:48:19.062 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 17.195908413 16:48:19.062 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 9.72 sec 16:48:19.064 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.44 minutes. Runtime.totalMemory()=2065170432 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr3 start:241603231 stop:241603272 contigLength:198295559 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-10/inputs/1547804351/0010-scattered.intervals -O output.vcf Job Mutect2.M2:5:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/tmp.a2d34b64 16:45:07.113 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:07.673 INFO GetSampleName - ------------------------------------------------------------ 16:45:07.674 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:07.674 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:07.674 INFO GetSampleName - Executing as root@189732452bc3 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:07.674 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:07.674 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:06 PM UTC 16:45:07.674 INFO GetSampleName - ------------------------------------------------------------ 16:45:07.674 INFO GetSampleName - ------------------------------------------------------------ 16:45:07.675 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:07.675 INFO GetSampleName - Picard Version: 2.18.7 16:45:07.675 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:07.675 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:07.676 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:07.676 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:07.676 INFO GetSampleName - Deflater: IntelDeflater 16:45:07.676 INFO GetSampleName - Inflater: IntelInflater 16:45:07.676 INFO GetSampleName - GCS max retries/reopens: 20 16:45:07.676 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:07.676 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:07.676 INFO GetSampleName - Initializing engine 16:45:13.539 INFO GetSampleName - Done initializing engine 16:45:13.591 INFO ProgressMeter - Starting traversal 16:45:13.592 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:13.593 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:13.594 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:13.594 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:13 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1787822080 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/tmp.a2d34b64 16:45:32.341 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:33.912 INFO GetSampleName - ------------------------------------------------------------ 16:45:33.912 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:33.912 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:33.912 INFO GetSampleName - Executing as root@189732452bc3 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:33.912 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:33.913 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:31 PM UTC 16:45:33.913 INFO GetSampleName - ------------------------------------------------------------ 16:45:33.913 INFO GetSampleName - ------------------------------------------------------------ 16:45:33.913 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:33.913 INFO GetSampleName - Picard Version: 2.18.7 16:45:33.914 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:33.914 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:33.914 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:33.914 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:33.914 INFO GetSampleName - Deflater: IntelDeflater 16:45:33.914 INFO GetSampleName - Inflater: IntelInflater 16:45:33.914 INFO GetSampleName - GCS max retries/reopens: 20 16:45:33.914 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:33.914 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:33.914 INFO GetSampleName - Initializing engine 16:45:39.129 INFO GetSampleName - Done initializing engine 16:45:39.191 INFO ProgressMeter - Starting traversal 16:45:39.192 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:39.193 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:39.193 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:39.193 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:39 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1717567488 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/tmp.a2d34b64 16:45:58.694 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:59.728 INFO Mutect2 - ------------------------------------------------------------ 16:45:59.743 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:59.743 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:59.743 INFO Mutect2 - Executing as root@189732452bc3 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:59.743 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:59.744 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:58 PM UTC 16:45:59.744 INFO Mutect2 - ------------------------------------------------------------ 16:45:59.744 INFO Mutect2 - ------------------------------------------------------------ 16:45:59.744 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:59.744 INFO Mutect2 - Picard Version: 2.18.7 16:45:59.744 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:59.750 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:59.750 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:59.750 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:59.750 INFO Mutect2 - Deflater: IntelDeflater 16:45:59.750 INFO Mutect2 - Inflater: IntelInflater 16:45:59.750 INFO Mutect2 - GCS max retries/reopens: 20 16:45:59.750 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:59.750 INFO Mutect2 - Initializing engine 16:46:05.555 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:08.125 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:08.481 INFO Mutect2 - Done initializing engine 16:46:08.829 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:08.902 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:09.039 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:09.040 INFO IntelPairHmm - Available threads: 24 16:46:09.040 INFO IntelPairHmm - Requested threads: 4 16:46:09.040 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:10.010 INFO ProgressMeter - Starting traversal 16:46:10.011 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:20.089 INFO ProgressMeter - chr2:72829486 0.2 190 1131.4 16:46:30.230 INFO ProgressMeter - chr2:73074493 0.3 1060 3145.6 16:46:40.250 INFO ProgressMeter - chr2:73234996 0.5 1630 3234.3 16:46:50.262 INFO ProgressMeter - chr2:73358196 0.7 2080 3100.5 16:47:00.461 INFO ProgressMeter - chr2:73614740 0.8 2980 3544.1 16:47:10.586 INFO ProgressMeter - chr2:73895707 1.0 3970 3932.3 16:47:20.674 INFO ProgressMeter - chr2:74249878 1.2 5260 4466.3 16:47:30.676 INFO ProgressMeter - chr2:75780790 1.3 10680 7944.0 16:47:40.701 INFO ProgressMeter - chr2:77366473 1.5 16200 10717.8 16:47:50.752 INFO ProgressMeter - chr2:78445775 1.7 19970 11894.0 16:48:00.773 INFO ProgressMeter - chr2:80304031 1.8 26470 14338.9 16:48:10.774 INFO ProgressMeter - chr2:81619689 2.0 31070 15436.8 16:48:20.777 INFO ProgressMeter - chr2:83849884 2.2 38880 17839.5 16:48:30.783 INFO ProgressMeter - chr2:85363249 2.3 44250 18860.3 16:48:40.817 INFO ProgressMeter - chr2:88132580 2.5 53950 21464.7 16:48:53.874 INFO ProgressMeter - chr2:89624079 2.7 59160 21662.1 16:49:03.897 INFO ProgressMeter - chr2:91559899 2.9 65900 22739.0 16:49:14.069 INFO ProgressMeter - chr2:91965542 3.1 67320 21945.3 16:49:24.109 INFO ProgressMeter - chr2:96284851 3.2 82130 25388.2 16:49:34.113 INFO ProgressMeter - chr2:98604041 3.4 90290 26542.6 16:49:49.135 INFO ProgressMeter - chr2:99101942 3.7 92050 25204.9 16:49:59.754 INFO ProgressMeter - chr2:99103467 3.8 92060 24042.5 16:50:09.761 INFO ProgressMeter - chr2:101814810 4.0 101640 25436.5 16:50:19.762 INFO ProgressMeter - chr2:104970737 4.2 112740 27084.6 16:50:30.797 INFO ProgressMeter - chr2:106247719 4.3 117280 26983.0 16:50:40.814 INFO ProgressMeter - chr2:108622200 4.5 125590 27826.1 16:50:50.822 INFO ProgressMeter - chr2:110714837 4.7 132890 28394.2 16:51:02.396 INFO ProgressMeter - chr2:110970593 4.9 133800 27456.9 16:51:13.682 INFO ProgressMeter - chr2:111126071 5.1 134350 26545.2 16:51:26.339 INFO ProgressMeter - chr2:111151211 5.3 134440 25500.1 16:51:39.082 INFO ProgressMeter - chr2:111153048 5.5 134450 24514.5 16:51:49.511 INFO ProgressMeter - chr2:111154771 5.7 134460 23763.2 16:51:59.534 INFO ProgressMeter - chr2:111573752 5.8 135920 23332.4 16:52:09.538 INFO ProgressMeter - chr2:115329659 6.0 149160 24892.7 16:52:19.554 INFO ProgressMeter - chr2:119516057 6.2 163830 26599.9 16:52:36.810 INFO ProgressMeter - chr2:121710542 6.4 171700 26634.0 16:52:46.811 INFO ProgressMeter - chr2:126156259 6.6 187290 28320.1 16:52:58.590 INFO ProgressMeter - chr2:128218515 6.8 194680 28588.9 16:53:11.271 INFO ProgressMeter - chr2:131188887 7.0 205180 29223.8 16:53:23.294 INFO ProgressMeter - chr2:131192103 7.2 205200 28415.6 16:53:34.509 INFO ProgressMeter - chr2:131196794 7.4 205220 27701.4 16:53:44.513 INFO ProgressMeter - chr2:134682738 7.6 217450 28706.2 16:53:47.690 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.142331 16:53:47.691 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 156.85497410300002 16:53:47.691 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 37.97 sec 16:53:47.691 INFO Mutect2 - Shutting down engine [October 8, 2018 4:53:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 7.82 minutes. Runtime.totalMemory()=2336751616 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr2 start:242938481 stop:242938521 contigLength:242193529 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-5/inputs/1547804351/0005-scattered.intervals -O output.vcf Job Mutect2.M2:37:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/tmp.768b36f2 16:45:11.271 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:12.153 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.153 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:12.167 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:12.169 INFO GetSampleName - Executing as root@d6b2e2c406fe on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:12.169 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:12.169 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:11 PM UTC 16:45:12.169 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.169 INFO GetSampleName - ------------------------------------------------------------ 16:45:12.170 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:12.170 INFO GetSampleName - Picard Version: 2.18.7 16:45:12.170 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:12.170 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:12.207 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:12.207 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:12.207 INFO GetSampleName - Deflater: IntelDeflater 16:45:12.207 INFO GetSampleName - Inflater: IntelInflater 16:45:12.207 INFO GetSampleName - GCS max retries/reopens: 20 16:45:12.207 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:12.209 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:12.209 INFO GetSampleName - Initializing engine 16:45:18.726 INFO GetSampleName - Done initializing engine 16:45:18.759 INFO ProgressMeter - Starting traversal 16:45:18.760 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:18.761 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:18.761 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:18.761 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1802502144 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/tmp.768b36f2 16:45:35.930 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:36.730 INFO GetSampleName - ------------------------------------------------------------ 16:45:36.731 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:36.731 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:36.731 INFO GetSampleName - Executing as root@d6b2e2c406fe on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:36.749 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:36.749 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:35 PM UTC 16:45:36.749 INFO GetSampleName - ------------------------------------------------------------ 16:45:36.749 INFO GetSampleName - ------------------------------------------------------------ 16:45:36.750 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:36.750 INFO GetSampleName - Picard Version: 2.18.7 16:45:36.750 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:36.750 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:36.750 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:36.750 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:36.751 INFO GetSampleName - Deflater: IntelDeflater 16:45:36.751 INFO GetSampleName - Inflater: IntelInflater 16:45:36.751 INFO GetSampleName - GCS max retries/reopens: 20 16:45:36.751 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:36.771 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:36.771 INFO GetSampleName - Initializing engine 16:45:42.612 INFO GetSampleName - Done initializing engine 16:45:42.671 INFO ProgressMeter - Starting traversal 16:45:42.672 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:42.673 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:42.673 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:42.674 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:42 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=1756364800 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/tmp.768b36f2 16:46:00.408 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:01.470 INFO Mutect2 - ------------------------------------------------------------ 16:46:01.470 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:01.470 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:01.470 INFO Mutect2 - Executing as root@d6b2e2c406fe on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:01.471 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:01.471 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:00 PM UTC 16:46:01.471 INFO Mutect2 - ------------------------------------------------------------ 16:46:01.471 INFO Mutect2 - ------------------------------------------------------------ 16:46:01.471 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:01.472 INFO Mutect2 - Picard Version: 2.18.7 16:46:01.472 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:01.472 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:01.472 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:01.472 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:01.472 INFO Mutect2 - Deflater: IntelDeflater 16:46:01.472 INFO Mutect2 - Inflater: IntelInflater 16:46:01.472 INFO Mutect2 - GCS max retries/reopens: 20 16:46:01.472 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:01.472 INFO Mutect2 - Initializing engine 16:46:08.077 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:10.428 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:10.841 INFO Mutect2 - Done initializing engine 16:46:11.280 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:11.355 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:11.500 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:11.500 INFO IntelPairHmm - Available threads: 24 16:46:11.500 INFO IntelPairHmm - Requested threads: 4 16:46:11.501 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:13.202 INFO ProgressMeter - Starting traversal 16:46:13.202 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:23.213 INFO ProgressMeter - chr15:82471083 0.2 290 1738.3 16:46:33.383 INFO ProgressMeter - chr15:82723637 0.3 1170 3478.5 16:46:43.939 INFO ProgressMeter - chr15:82903210 0.5 1800 3513.7 16:46:55.125 INFO ProgressMeter - chr15:83025201 0.7 2240 3205.9 16:47:05.200 INFO ProgressMeter - chr15:83231227 0.9 2970 3427.1 16:47:15.783 INFO ProgressMeter - chr15:83459925 1.0 3770 3614.6 16:47:26.404 INFO ProgressMeter - chr15:83771028 1.2 4860 3983.5 16:47:36.489 INFO ProgressMeter - chr15:84546056 1.4 7510 5410.2 16:47:46.512 INFO ProgressMeter - chr15:85862403 1.6 12130 7799.8 16:47:46.902 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036091642 16:47:46.902 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 4.066503745 16:47:46.902 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 3.20 sec 16:47:46.903 INFO Mutect2 - Shutting down engine [October 8, 2018 4:47:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 1.78 minutes. Runtime.totalMemory()=2042101760 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr15 start:145857986 stop:145858045 contigLength:101991189 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-37/inputs/1547804351/0037-scattered.intervals -O output.vcf Job Mutect2.M2:19:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/tmp.bfc41406 16:45:10.679 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:11.587 INFO GetSampleName - ------------------------------------------------------------ 16:45:11.588 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:11.614 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:11.624 INFO GetSampleName - Executing as root@096c18aca0c9 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:11.624 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:11.624 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:10 PM UTC 16:45:11.624 INFO GetSampleName - ------------------------------------------------------------ 16:45:11.624 INFO GetSampleName - ------------------------------------------------------------ 16:45:11.625 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:11.625 INFO GetSampleName - Picard Version: 2.18.7 16:45:11.625 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:11.625 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:11.644 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:11.644 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:11.644 INFO GetSampleName - Deflater: IntelDeflater 16:45:11.644 INFO GetSampleName - Inflater: IntelInflater 16:45:11.644 INFO GetSampleName - GCS max retries/reopens: 20 16:45:11.644 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:11.646 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:11.646 INFO GetSampleName - Initializing engine 16:45:17.745 INFO GetSampleName - Done initializing engine 16:45:17.809 INFO ProgressMeter - Starting traversal 16:45:17.809 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:17.810 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:17.811 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:17.811 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:17 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1804599296 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/tmp.bfc41406 16:45:36.693 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:37.473 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.474 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:37.474 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:37.474 INFO GetSampleName - Executing as root@096c18aca0c9 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:37.474 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:37.475 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:36 PM UTC 16:45:37.475 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.475 INFO GetSampleName - ------------------------------------------------------------ 16:45:37.475 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:37.475 INFO GetSampleName - Picard Version: 2.18.7 16:45:37.487 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:37.488 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:37.488 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:37.488 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:37.488 INFO GetSampleName - Deflater: IntelDeflater 16:45:37.488 INFO GetSampleName - Inflater: IntelInflater 16:45:37.488 INFO GetSampleName - GCS max retries/reopens: 20 16:45:37.488 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:37.488 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:37.489 INFO GetSampleName - Initializing engine 16:45:43.431 INFO GetSampleName - Done initializing engine 16:45:43.493 INFO ProgressMeter - Starting traversal 16:45:43.494 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:43.495 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:43.495 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:43.495 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:43 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1791492096 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/tmp.bfc41406 16:46:01.723 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:02.750 INFO Mutect2 - ------------------------------------------------------------ 16:46:02.750 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:02.752 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:02.760 INFO Mutect2 - Executing as root@096c18aca0c9 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:02.761 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:02.762 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:01 PM UTC 16:46:02.762 INFO Mutect2 - ------------------------------------------------------------ 16:46:02.762 INFO Mutect2 - ------------------------------------------------------------ 16:46:02.762 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:02.762 INFO Mutect2 - Picard Version: 2.18.7 16:46:02.763 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:02.763 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:02.773 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:02.773 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:02.773 INFO Mutect2 - Deflater: IntelDeflater 16:46:02.773 INFO Mutect2 - Inflater: IntelInflater 16:46:02.773 INFO Mutect2 - GCS max retries/reopens: 20 16:46:02.773 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:02.774 INFO Mutect2 - Initializing engine 16:46:09.917 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:12.620 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:12.964 INFO Mutect2 - Done initializing engine 16:46:13.391 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:13.405 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:13.581 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:13.582 INFO IntelPairHmm - Available threads: 24 16:46:13.582 INFO IntelPairHmm - Requested threads: 4 16:46:13.582 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:15.459 INFO ProgressMeter - Starting traversal 16:46:15.483 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:25.840 INFO ProgressMeter - chr6:161458832 0.2 230 1340.2 16:46:33.297 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005070805 16:46:33.297 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.330303882 16:46:33.298 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.41 sec 16:46:33.299 INFO Mutect2 - Shutting down engine [October 8, 2018 4:46:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.53 minutes. Runtime.totalMemory()=2011168768 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr6 start:253376095 stop:253376188 contigLength:170805979 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-19/inputs/1547804351/0019-scattered.intervals -O output.vcf Job Mutect2.M2:15:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/tmp.36af897e 16:45:11.107 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:13.261 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.262 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:13.262 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:13.262 INFO GetSampleName - Executing as root@6a436cfffe67 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:13.262 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:13.262 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:10 PM UTC 16:45:13.263 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.263 INFO GetSampleName - ------------------------------------------------------------ 16:45:13.263 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:13.263 INFO GetSampleName - Picard Version: 2.18.7 16:45:13.264 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:13.264 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:13.264 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:13.264 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:13.264 INFO GetSampleName - Deflater: IntelDeflater 16:45:13.264 INFO GetSampleName - Inflater: IntelInflater 16:45:13.264 INFO GetSampleName - GCS max retries/reopens: 20 16:45:13.264 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:13.264 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:13.264 INFO GetSampleName - Initializing engine 16:45:19.492 INFO GetSampleName - Done initializing engine 16:45:19.546 INFO ProgressMeter - Starting traversal 16:45:19.547 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:19.549 INFO ProgressMeter - unmapped 0.0 0 0.0 16:45:19.562 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:19.562 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.15 minutes. Runtime.totalMemory()=1865416704 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/tmp.36af897e 16:45:37.981 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:38.700 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.730 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:38.730 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:38.739 INFO GetSampleName - Executing as root@6a436cfffe67 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:38.739 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:38.740 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:37 PM UTC 16:45:38.740 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.740 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.741 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:38.741 INFO GetSampleName - Picard Version: 2.18.7 16:45:38.741 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:38.741 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:38.760 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:38.760 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:38.760 INFO GetSampleName - Deflater: IntelDeflater 16:45:38.760 INFO GetSampleName - Inflater: IntelInflater 16:45:38.761 INFO GetSampleName - GCS max retries/reopens: 20 16:45:38.761 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:38.771 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:38.772 INFO GetSampleName - Initializing engine 16:45:45.414 INFO GetSampleName - Done initializing engine 16:45:45.482 INFO ProgressMeter - Starting traversal 16:45:45.483 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:45.486 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:45.487 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:45.487 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:45 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1873805312 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/tmp.36af897e 16:46:03.540 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:04.680 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.680 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:04.681 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:04.682 INFO Mutect2 - Executing as root@6a436cfffe67 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:04.696 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:04.696 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:03 PM UTC 16:46:04.696 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.696 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.712 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:04.712 INFO Mutect2 - Picard Version: 2.18.7 16:46:04.712 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:04.712 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:04.713 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:04.713 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:04.713 INFO Mutect2 - Deflater: IntelDeflater 16:46:04.713 INFO Mutect2 - Inflater: IntelInflater 16:46:04.713 INFO Mutect2 - GCS max retries/reopens: 20 16:46:04.713 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:04.713 INFO Mutect2 - Initializing engine 16:46:12.060 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:14.620 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:14.881 INFO Mutect2 - Done initializing engine 16:46:15.320 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:15.363 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:15.551 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:15.552 INFO IntelPairHmm - Available threads: 24 16:46:15.552 INFO IntelPairHmm - Requested threads: 4 16:46:15.552 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:16.884 INFO ProgressMeter - Starting traversal 16:46:16.884 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:27.242 INFO ProgressMeter - chr5:85592283 0.2 170 988.9 16:46:37.310 INFO ProgressMeter - chr5:85979286 0.3 1500 4406.4 16:46:47.427 INFO ProgressMeter - chr5:86223907 0.5 2350 4616.4 16:46:57.463 INFO ProgressMeter - chr5:86460741 0.7 3180 4701.9 16:47:07.702 INFO ProgressMeter - chr5:86764370 0.8 4240 5006.2 16:47:17.793 INFO ProgressMeter - chr5:87091576 1.0 5380 5299.8 16:47:27.843 INFO ProgressMeter - chr5:87671136 1.2 7400 6257.1 16:47:38.056 INFO ProgressMeter - chr5:88627762 1.4 10730 7931.3 16:47:48.071 INFO ProgressMeter - chr5:90229960 1.5 16300 10725.2 16:47:58.071 INFO ProgressMeter - chr5:91386474 1.7 20340 12060.8 16:48:08.081 INFO ProgressMeter - chr5:92647409 1.9 24740 13349.3 16:48:52.319 INFO ProgressMeter - chr5:93683492 2.6 28360 10947.3 16:49:02.365 INFO ProgressMeter - chr5:94877318 2.8 32540 11798.3 16:49:12.372 INFO ProgressMeter - chr5:97414833 2.9 41440 14168.5 16:49:22.487 INFO ProgressMeter - chr5:100603226 3.1 52520 16978.2 16:49:32.507 INFO ProgressMeter - chr5:104163953 3.3 64890 19902.6 16:49:42.526 INFO ProgressMeter - chr5:108705277 3.4 80580 23510.9 16:49:52.529 INFO ProgressMeter - chr5:111727102 3.6 91150 25361.1 16:50:14.353 INFO ProgressMeter - chr5:112767946 4.0 94800 23952.6 16:50:26.276 INFO ProgressMeter - chr5:112794242 4.2 94900 22831.5 16:50:40.949 INFO ProgressMeter - chr5:112817801 4.4 94990 21583.3 16:50:51.161 INFO ProgressMeter - chr5:112830073 4.6 95050 20792.8 16:51:01.193 INFO ProgressMeter - chr5:112838300 4.7 95090 20067.6 16:51:18.575 INFO ProgressMeter - chr5:112839372 5.0 95100 18913.4 16:51:42.567 INFO ProgressMeter - chr5:112841022 5.4 95110 17521.9 16:52:13.367 INFO ProgressMeter - chr5:112842491 5.9 95120 16009.7 16:52:47.533 INFO ProgressMeter - chr5:112844103 6.5 95130 14611.1 16:52:50.660 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.12419274500000001 16:52:50.660 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 173.60143817800002 16:52:50.660 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 37.13 sec 16:52:50.661 INFO Mutect2 - Shutting down engine [October 8, 2018 4:52:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 6.79 minutes. Runtime.totalMemory()=2069889024 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr5 start:191999778 stop:191999862 contigLength:181538259 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-15/inputs/1547804351/0015-scattered.intervals -O output.vcf Job Mutect2.M2:44:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/tmp.d381fab9 16:45:08.471 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:09.358 INFO GetSampleName - ------------------------------------------------------------ 16:45:09.358 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:09.358 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:09.378 INFO GetSampleName - Executing as root@d975c8756e9d on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:09.378 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:09.378 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:08 PM UTC 16:45:09.378 INFO GetSampleName - ------------------------------------------------------------ 16:45:09.378 INFO GetSampleName - ------------------------------------------------------------ 16:45:09.379 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:09.379 INFO GetSampleName - Picard Version: 2.18.7 16:45:09.379 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:09.379 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:09.380 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:09.380 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:09.380 INFO GetSampleName - Deflater: IntelDeflater 16:45:09.380 INFO GetSampleName - Inflater: IntelInflater 16:45:09.380 INFO GetSampleName - GCS max retries/reopens: 20 16:45:09.380 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:09.380 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:09.380 INFO GetSampleName - Initializing engine 16:45:15.729 INFO GetSampleName - Done initializing engine 16:45:15.784 INFO ProgressMeter - Starting traversal 16:45:15.785 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:15.786 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:15.787 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:15.787 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:15 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1752170496 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/tmp.d381fab9 16:45:33.078 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:34.006 INFO GetSampleName - ------------------------------------------------------------ 16:45:34.006 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:34.006 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:34.007 INFO GetSampleName - Executing as root@d975c8756e9d on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:34.007 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:34.007 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:32 PM UTC 16:45:34.007 INFO GetSampleName - ------------------------------------------------------------ 16:45:34.007 INFO GetSampleName - ------------------------------------------------------------ 16:45:34.024 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:34.024 INFO GetSampleName - Picard Version: 2.18.7 16:45:34.024 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:34.025 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:34.025 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:34.025 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:34.025 INFO GetSampleName - Deflater: IntelDeflater 16:45:34.025 INFO GetSampleName - Inflater: IntelInflater 16:45:34.025 INFO GetSampleName - GCS max retries/reopens: 20 16:45:34.025 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:34.025 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:34.025 INFO GetSampleName - Initializing engine 16:45:39.880 INFO GetSampleName - Done initializing engine 16:45:39.931 INFO ProgressMeter - Starting traversal 16:45:39.932 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:39.937 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:39.938 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:39.938 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:39 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1880621056 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/tmp.d381fab9 16:45:57.957 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:59.129 INFO Mutect2 - ------------------------------------------------------------ 16:45:59.130 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:59.130 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:59.130 INFO Mutect2 - Executing as root@d975c8756e9d on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:59.130 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:59.131 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:57 PM UTC 16:45:59.154 INFO Mutect2 - ------------------------------------------------------------ 16:45:59.154 INFO Mutect2 - ------------------------------------------------------------ 16:45:59.154 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:59.154 INFO Mutect2 - Picard Version: 2.18.7 16:45:59.155 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:59.155 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:59.155 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:59.155 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:59.155 INFO Mutect2 - Deflater: IntelDeflater 16:45:59.155 INFO Mutect2 - Inflater: IntelInflater 16:45:59.155 INFO Mutect2 - GCS max retries/reopens: 20 16:45:59.155 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:59.155 INFO Mutect2 - Initializing engine 16:46:05.548 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:07.744 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:07.952 INFO Mutect2 - Done initializing engine 16:46:08.313 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:08.338 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:08.475 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:08.476 INFO IntelPairHmm - Available threads: 24 16:46:08.476 INFO IntelPairHmm - Requested threads: 4 16:46:08.476 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:09.513 INFO ProgressMeter - Starting traversal 16:46:09.514 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:19.686 INFO ProgressMeter - chr22:10591554 0.2 11700 69278.6 16:46:30.617 INFO ProgressMeter - chr22:10727936 0.4 12180 34753.7 16:46:57.153 INFO ProgressMeter - chr22:10754160 0.8 12280 15466.3 16:47:07.265 INFO ProgressMeter - chr22:10957358 1.0 12990 13495.9 16:47:17.290 INFO ProgressMeter - chr22:11077052 1.1 13410 11871.6 16:47:27.895 INFO ProgressMeter - chr22:11338968 1.3 14300 10946.5 16:47:37.941 INFO ProgressMeter - chr22:11938896 1.5 16370 11107.5 16:47:47.945 INFO ProgressMeter - chr22:14379838 1.6 24590 14989.3 16:48:10.457 INFO ProgressMeter - chr22:15627643 2.0 28770 14272.8 16:48:21.238 INFO ProgressMeter - chr22:15629608 2.2 28780 13109.2 16:48:31.243 INFO ProgressMeter - chr22:15690645 2.4 28990 12272.7 16:49:05.307 INFO ProgressMeter - chr22:16573190 2.9 32050 10939.0 16:49:20.072 INFO ProgressMeter - chr22:16574657 3.2 32060 10094.6 16:49:30.072 INFO ProgressMeter - chr22:18198750 3.3 37980 11362.3 16:49:40.100 INFO ProgressMeter - chr22:20181236 3.5 45110 12852.7 16:49:50.127 INFO ProgressMeter - chr22:22086330 3.7 52040 14153.3 16:50:07.821 INFO ProgressMeter - chr22:23802113 4.0 58300 14678.5 16:50:17.827 INFO ProgressMeter - chr22:24118115 4.1 59460 14367.4 16:50:27.838 INFO ProgressMeter - chr22:26291978 4.3 67390 15652.4 16:50:37.841 INFO ProgressMeter - chr22:28585877 4.5 75730 16933.8 16:50:47.893 INFO ProgressMeter - chr22:28694843 4.6 76130 16408.6 16:51:08.652 INFO ProgressMeter - chr22:28696805 5.0 76140 15271.9 16:51:21.333 INFO ProgressMeter - chr22:28711695 5.2 76210 14664.3 16:51:32.222 INFO ProgressMeter - chr22:28721069 5.4 76250 14176.9 16:51:46.555 INFO ProgressMeter - chr22:28736643 5.6 76310 13584.7 16:52:01.222 INFO ProgressMeter - chr22:29638237 5.9 79610 13581.2 16:52:15.047 INFO ProgressMeter - chr22:29642703 6.1 79630 13070.8 16:52:25.330 INFO ProgressMeter - chr22:29665986 6.3 79720 12727.5 16:52:52.888 INFO ProgressMeter - chr22:29683096 6.7 79790 11868.4 16:53:10.573 INFO ProgressMeter - chr22:31757210 7.0 87480 12465.7 16:53:25.206 INFO ProgressMeter - chr22:31761637 7.3 87500 12049.8 16:53:36.969 INFO ProgressMeter - chr22:31770882 7.5 87540 11738.4 16:53:47.719 INFO ProgressMeter - chr22:31783780 7.6 87600 11470.8 16:54:09.429 INFO ProgressMeter - chr22:31792266 8.0 87640 10956.9 16:54:20.541 INFO ProgressMeter - chr22:31794002 8.2 87650 10710.2 16:54:33.691 INFO ProgressMeter - chr22:31802899 8.4 87690 10435.6 16:54:50.137 INFO ProgressMeter - chr22:31806020 8.7 87710 10108.3 16:55:04.833 INFO ProgressMeter - chr22:31810122 8.9 87730 9833.0 16:55:23.264 INFO ProgressMeter - chr22:31816829 9.2 87760 9509.0 16:55:34.403 INFO ProgressMeter - chr22:31834890 9.4 87830 9328.9 16:55:48.346 INFO ProgressMeter - chr22:31843883 9.6 87870 9108.3 16:56:01.015 INFO ProgressMeter - chr22:31873193 9.9 88000 8926.4 16:56:15.351 INFO ProgressMeter - chr22:31906543 10.1 88140 8729.1 16:56:25.352 INFO ProgressMeter - chr22:37774339 10.3 109700 10687.9 16:56:38.871 INFO ProgressMeter - chr22:41126061 10.5 122160 11646.2 16:56:49.384 INFO ProgressMeter - chr22:41141712 10.7 122240 11462.3 16:57:01.714 INFO ProgressMeter - chr22:41151246 10.9 122280 11249.3 16:57:13.103 INFO ProgressMeter - chr22:41169535 11.1 122370 11064.4 16:57:25.702 INFO ProgressMeter - chr22:41178453 11.3 122420 10862.7 16:57:37.018 INFO ProgressMeter - chr22:42777375 11.5 128380 11204.0 16:57:37.258 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.209078324 16:57:37.259 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 402.122699242 16:57:37.259 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 84.63 sec 16:57:37.259 INFO Mutect2 - Shutting down engine [October 8, 2018 4:57:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 11.66 minutes. Runtime.totalMemory()=2110783488 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr22 start:56926369 stop:56926414 contigLength:50818468 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-44/inputs/1547804351/0044-scattered.intervals -O output.vcf Job Mutect2.M2:7:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/tmp.99534a94 16:44:57.384 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:44:58.222 INFO GetSampleName - ------------------------------------------------------------ 16:44:58.222 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:44:58.222 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:44:58.223 INFO GetSampleName - Executing as root@2f7ce8491be8 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:44:58.223 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:44:58.223 INFO GetSampleName - Start Date/Time: October 8, 2018 4:44:57 PM UTC 16:44:58.223 INFO GetSampleName - ------------------------------------------------------------ 16:44:58.223 INFO GetSampleName - ------------------------------------------------------------ 16:44:58.246 INFO GetSampleName - HTSJDK Version: 2.16.0 16:44:58.246 INFO GetSampleName - Picard Version: 2.18.7 16:44:58.247 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:44:58.247 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:44:58.251 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:44:58.251 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:44:58.251 INFO GetSampleName - Deflater: IntelDeflater 16:44:58.251 INFO GetSampleName - Inflater: IntelInflater 16:44:58.251 INFO GetSampleName - GCS max retries/reopens: 20 16:44:58.251 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:44:58.252 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:44:58.252 INFO GetSampleName - Initializing engine 16:45:04.679 INFO GetSampleName - Done initializing engine 16:45:04.722 INFO ProgressMeter - Starting traversal 16:45:04.723 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:04.724 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:04.724 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:04.724 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:04 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1744830464 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/tmp.99534a94 16:45:21.564 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:23.212 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.212 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:23.212 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:23.214 INFO GetSampleName - Executing as root@2f7ce8491be8 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:23.215 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:23.215 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:21 PM UTC 16:45:23.215 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.215 INFO GetSampleName - ------------------------------------------------------------ 16:45:23.216 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:23.216 INFO GetSampleName - Picard Version: 2.18.7 16:45:23.216 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:23.216 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:23.216 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:23.216 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:23.216 INFO GetSampleName - Deflater: IntelDeflater 16:45:23.216 INFO GetSampleName - Inflater: IntelInflater 16:45:23.216 INFO GetSampleName - GCS max retries/reopens: 20 16:45:23.217 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:23.217 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:23.217 INFO GetSampleName - Initializing engine 16:45:28.956 INFO GetSampleName - Done initializing engine 16:45:29.008 INFO ProgressMeter - Starting traversal 16:45:29.009 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:29.010 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:29.011 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:29.011 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:29 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1797783552 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/tmp.99534a94 16:45:48.167 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:49.119 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.119 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:49.144 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:49.146 INFO Mutect2 - Executing as root@2f7ce8491be8 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:49.152 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:49.152 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:48 PM UTC 16:45:49.152 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.152 INFO Mutect2 - ------------------------------------------------------------ 16:45:49.165 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:49.165 INFO Mutect2 - Picard Version: 2.18.7 16:45:49.165 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:49.166 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:49.178 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:49.178 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:49.178 INFO Mutect2 - Deflater: IntelDeflater 16:45:49.178 INFO Mutect2 - Inflater: IntelInflater 16:45:49.178 INFO Mutect2 - GCS max retries/reopens: 20 16:45:49.178 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:49.178 INFO Mutect2 - Initializing engine 16:45:55.667 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:45:57.886 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:45:58.268 INFO Mutect2 - Done initializing engine 16:45:58.739 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:45:58.748 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:45:59.022 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:45:59.024 INFO IntelPairHmm - Available threads: 24 16:45:59.024 INFO IntelPairHmm - Requested threads: 4 16:45:59.025 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:00.362 INFO ProgressMeter - Starting traversal 16:46:00.362 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:11.141 INFO ProgressMeter - chr2:201545599 0.2 260 1452.4 16:46:21.312 INFO ProgressMeter - chr2:201772320 0.3 1060 3035.8 16:46:31.429 INFO ProgressMeter - chr2:202041720 0.5 2010 3889.1 16:46:41.396 INFO ProgressMeter - chr2:202264195 0.7 2800 4094.2 16:46:53.561 INFO ProgressMeter - chr2:202504970 0.9 3660 4127.9 16:47:03.570 INFO ProgressMeter - chr2:202749620 1.1 4540 4309.6 16:47:13.596 INFO ProgressMeter - chr2:203024174 1.2 5510 4514.3 16:47:28.957 INFO ProgressMeter - chr2:203772612 1.5 8180 5539.8 16:48:03.961 INFO ProgressMeter - chr2:203774892 2.1 8190 3975.8 16:48:13.970 INFO ProgressMeter - chr2:205967890 2.2 15880 7131.3 16:48:15.081 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.204267253 16:48:15.081 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 22.996061871000002 16:48:15.081 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 18.89 sec 16:48:15.082 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.45 minutes. Runtime.totalMemory()=2037907456 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr2 start:272744137 stop:272744184 contigLength:242193529 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-7/inputs/1547804351/0007-scattered.intervals -O output.vcf Job Mutect2.M2:13:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/tmp.249c8404 16:45:12.474 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:14.037 INFO GetSampleName - ------------------------------------------------------------ 16:45:14.037 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:14.037 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:14.037 INFO GetSampleName - Executing as root@503eb95c481e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:14.038 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:14.038 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:12 PM UTC 16:45:14.038 INFO GetSampleName - ------------------------------------------------------------ 16:45:14.038 INFO GetSampleName - ------------------------------------------------------------ 16:45:14.039 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:14.039 INFO GetSampleName - Picard Version: 2.18.7 16:45:14.039 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:14.039 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:14.039 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:14.039 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:14.039 INFO GetSampleName - Deflater: IntelDeflater 16:45:14.039 INFO GetSampleName - Inflater: IntelInflater 16:45:14.039 INFO GetSampleName - GCS max retries/reopens: 20 16:45:14.039 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:14.040 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:14.040 INFO GetSampleName - Initializing engine 16:45:20.020 INFO GetSampleName - Done initializing engine 16:45:20.066 INFO ProgressMeter - Starting traversal 16:45:20.069 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:20.071 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:20.071 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:20.071 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:20 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1796734976 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/tmp.249c8404 16:45:37.105 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:38.223 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.223 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:38.223 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:38.235 INFO GetSampleName - Executing as root@503eb95c481e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:38.255 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:38.255 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:36 PM UTC 16:45:38.255 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.255 INFO GetSampleName - ------------------------------------------------------------ 16:45:38.256 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:38.256 INFO GetSampleName - Picard Version: 2.18.7 16:45:38.256 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:38.256 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:38.257 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:38.257 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:38.257 INFO GetSampleName - Deflater: IntelDeflater 16:45:38.257 INFO GetSampleName - Inflater: IntelInflater 16:45:38.257 INFO GetSampleName - GCS max retries/reopens: 20 16:45:38.257 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:38.279 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:38.280 INFO GetSampleName - Initializing engine 16:45:44.385 INFO GetSampleName - Done initializing engine 16:45:44.423 INFO ProgressMeter - Starting traversal 16:45:44.424 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:44.426 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:44.426 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:44.426 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:44 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1784676352 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/tmp.249c8404 16:46:03.319 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:46:04.475 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.475 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:46:04.482 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:46:04.483 INFO Mutect2 - Executing as root@503eb95c481e on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:46:04.504 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:46:04.506 INFO Mutect2 - Start Date/Time: October 8, 2018 4:46:03 PM UTC 16:46:04.506 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.506 INFO Mutect2 - ------------------------------------------------------------ 16:46:04.525 INFO Mutect2 - HTSJDK Version: 2.16.0 16:46:04.525 INFO Mutect2 - Picard Version: 2.18.7 16:46:04.525 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:46:04.526 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:46:04.526 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:46:04.526 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:46:04.526 INFO Mutect2 - Deflater: IntelDeflater 16:46:04.526 INFO Mutect2 - Inflater: IntelInflater 16:46:04.526 INFO Mutect2 - GCS max retries/reopens: 20 16:46:04.526 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:46:04.527 INFO Mutect2 - Initializing engine 16:46:11.786 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:14.433 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:14.614 INFO Mutect2 - Done initializing engine 16:46:15.011 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:15.049 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:15.222 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:15.223 INFO IntelPairHmm - Available threads: 24 16:46:15.223 INFO IntelPairHmm - Requested threads: 4 16:46:15.223 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:16.423 INFO ProgressMeter - Starting traversal 16:46:16.423 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:26.629 INFO ProgressMeter - chr4:147225237 0.2 550 3243.9 16:46:36.626 INFO ProgressMeter - chr4:147620271 0.3 1900 5643.3 16:46:46.632 INFO ProgressMeter - chr4:147856804 0.5 2720 5402.5 16:46:56.934 INFO ProgressMeter - chr4:148191914 0.7 3870 5731.9 16:47:07.253 INFO ProgressMeter - chr4:148528086 0.8 5020 5925.8 16:47:17.443 INFO ProgressMeter - chr4:148881333 1.0 6230 6126.0 16:47:27.462 INFO ProgressMeter - chr4:149520877 1.2 8410 7103.2 16:47:37.674 INFO ProgressMeter - chr4:150387729 1.4 11390 8414.6 16:47:47.665 INFO ProgressMeter - chr4:151675899 1.5 15830 10409.8 16:48:06.998 INFO ProgressMeter - chr4:152324438 1.8 18070 9805.2 16:48:20.058 INFO ProgressMeter - chr4:152326646 2.1 18080 8774.3 16:48:30.911 INFO ProgressMeter - chr4:152338026 2.2 18130 8088.5 16:48:45.583 INFO ProgressMeter - chr4:152352692 2.5 18190 7317.0 16:49:10.037 INFO ProgressMeter - chr4:152411371 2.9 18400 6359.1 16:49:26.586 INFO ProgressMeter - chr4:152413789 3.2 18410 5808.7 16:49:36.587 INFO ProgressMeter - chr4:155493850 3.3 29060 8710.9 16:49:46.587 INFO ProgressMeter - chr4:158489545 3.5 39370 11239.8 16:49:56.178 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.099663184 16:49:56.178 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 71.877505895 16:49:56.178 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 15.67 sec 16:49:56.179 INFO Mutect2 - Shutting down engine [October 8, 2018 4:49:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 3.88 minutes. Runtime.totalMemory()=2058354688 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr4 start:276856324 stop:276856370 contigLength:190214555 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-13/inputs/1547804351/0013-scattered.intervals -O output.vcf Job Mutect2.M2:30:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /bdp-picb/bioinfo/gyzheng/GATK_pipeline/GATK_resource/test7/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/tmp.23a8374a 16:45:07.107 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:08.066 INFO GetSampleName - ------------------------------------------------------------ 16:45:08.067 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:08.067 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:08.067 INFO GetSampleName - Executing as root@238043e92ef9 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:08.067 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:08.067 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:06 PM UTC 16:45:08.068 INFO GetSampleName - ------------------------------------------------------------ 16:45:08.068 INFO GetSampleName - ------------------------------------------------------------ 16:45:08.068 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:08.068 INFO GetSampleName - Picard Version: 2.18.7 16:45:08.077 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:08.077 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:08.078 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:08.078 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:08.078 INFO GetSampleName - Deflater: IntelDeflater 16:45:08.078 INFO GetSampleName - Inflater: IntelInflater 16:45:08.078 INFO GetSampleName - GCS max retries/reopens: 20 16:45:08.078 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:08.106 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:08.106 INFO GetSampleName - Initializing engine 16:45:14.378 INFO GetSampleName - Done initializing engine 16:45:14.412 INFO ProgressMeter - Starting traversal 16:45:14.413 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:14.415 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:14.416 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:14.416 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:14 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1722286080 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestT.hg38.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/tmp.23a8374a 16:45:31.603 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:32.427 INFO GetSampleName - ------------------------------------------------------------ 16:45:32.428 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:32.428 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:32.428 INFO GetSampleName - Executing as root@238043e92ef9 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:32.428 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:32.428 INFO GetSampleName - Start Date/Time: October 8, 2018 4:45:31 PM UTC 16:45:32.428 INFO GetSampleName - ------------------------------------------------------------ 16:45:32.428 INFO GetSampleName - ------------------------------------------------------------ 16:45:32.449 INFO GetSampleName - HTSJDK Version: 2.16.0 16:45:32.449 INFO GetSampleName - Picard Version: 2.18.7 16:45:32.449 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:32.449 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:32.449 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:32.449 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:32.449 INFO GetSampleName - Deflater: IntelDeflater 16:45:32.449 INFO GetSampleName - Inflater: IntelInflater 16:45:32.450 INFO GetSampleName - GCS max retries/reopens: 20 16:45:32.450 INFO GetSampleName - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:32.450 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 16:45:32.450 INFO GetSampleName - Initializing engine 16:45:38.525 INFO GetSampleName - Done initializing engine 16:45:38.573 INFO ProgressMeter - Starting traversal 16:45:38.574 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 16:45:38.575 INFO ProgressMeter - unmapped 0.0 0 NaN 16:45:38.575 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 16:45:38.575 INFO GetSampleName - Shutting down engine [October 8, 2018 4:45:38 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1784152064 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestN.hg38.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/tmp.23a8374a 16:45:57.167 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:45:58.342 INFO Mutect2 - ------------------------------------------------------------ 16:45:58.342 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.7.0 16:45:58.342 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:45:58.343 INFO Mutect2 - Executing as root@238043e92ef9 on Linux v3.10.0-693.21.1.el7.x86_64 amd64 16:45:58.343 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 16:45:58.343 INFO Mutect2 - Start Date/Time: October 8, 2018 4:45:56 PM UTC 16:45:58.343 INFO Mutect2 - ------------------------------------------------------------ 16:45:58.343 INFO Mutect2 - ------------------------------------------------------------ 16:45:58.344 INFO Mutect2 - HTSJDK Version: 2.16.0 16:45:58.344 INFO Mutect2 - Picard Version: 2.18.7 16:45:58.344 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:45:58.344 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:45:58.344 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:45:58.344 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:45:58.344 INFO Mutect2 - Deflater: IntelDeflater 16:45:58.344 INFO Mutect2 - Inflater: IntelInflater 16:45:58.344 INFO Mutect2 - GCS max retries/reopens: 20 16:45:58.344 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 16:45:58.344 INFO Mutect2 - Initializing engine 16:46:05.568 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/1437983679/af-only-gnomad.hg38.vcf.gz 16:46:08.043 INFO IntervalArgumentCollection - Processing 64346938 bp from intervals 16:46:08.334 INFO Mutect2 - Done initializing engine 16:46:08.840 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:46:08.960 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:46:09.131 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:46:09.131 INFO IntelPairHmm - Available threads: 24 16:46:09.131 INFO IntelPairHmm - Requested threads: 4 16:46:09.131 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:46:10.426 INFO ProgressMeter - Starting traversal 16:46:10.427 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:46:20.678 INFO ProgressMeter - chr11:121773876 0.2 170 998.6 16:46:30.956 INFO ProgressMeter - chr11:121994374 0.3 950 2776.6 16:46:41.075 INFO ProgressMeter - chr11:122187308 0.5 1630 3191.1 16:46:52.414 INFO ProgressMeter - chr11:122384523 0.7 2330 3331.2 16:47:02.440 INFO ProgressMeter - chr11:122512605 0.9 2800 3230.0 16:47:12.843 INFO ProgressMeter - chr11:122648112 1.0 3300 3172.3 16:47:22.860 INFO ProgressMeter - chr11:122843969 1.2 4000 3313.5 16:47:32.923 INFO ProgressMeter - chr11:123252144 1.4 5450 3963.8 16:47:42.939 INFO ProgressMeter - chr11:124630555 1.5 10340 6706.2 16:47:52.968 INFO ProgressMeter - chr11:125602507 1.7 13860 8109.9 16:48:03.020 INFO ProgressMeter - chr11:126225495 1.9 16090 8574.2 16:48:13.123 INFO ProgressMeter - chr11:127730345 2.0 21470 10499.1 16:48:23.126 INFO ProgressMeter - chr11:128713044 2.2 24950 11281.2 16:48:33.146 INFO ProgressMeter - chr11:130253659 2.4 30510 12826.6 16:48:43.187 INFO ProgressMeter - chr11:131925027 2.5 36440 14312.6 16:48:51.500 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.120224093 16:48:51.501 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 14.185400996 16:48:51.501 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 4.66 sec 16:48:51.503 INFO Mutect2 - Shutting down engine [October 8, 2018 4:48:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 2.91 minutes. Runtime.totalMemory()=1940389888 htsjdk.samtools.SAMException: Query asks for data past end of contig. Query contig chr11 start:220744338 stop:220744386 contigLength:135086622 at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:303) at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:80) at org.broadinstitute.hellbender.engine.ReferenceDataSource.queryAndPrefetch(ReferenceDataSource.java:64) at org.broadinstitute.hellbender.engine.ReferenceDataSource.query(ReferenceDataSource.java:90) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:101) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42) at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315) at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69) at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-1601801936/Homo_sapiens_assembly38.fasta -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestT.hg38.bam -tumor mytestT -I /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/-314364064/mytestN.hg38.bam -normal mytestN --germline-resource /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/1437983679/af-only-gnomad.hg38.vcf.gz -L /cromwell-executions/Mutect2/ec34099b-7f45-4a33-b205-0cd6011f53f0/call-M2/shard-30/inputs/1547804351/0030-scattered.intervals -O output.vcf [2018-10-09 01:01:14,80] [info] WorkflowManagerActor WorkflowActor-ec34099b-7f45-4a33-b205-0cd6011f53f0 is in a terminal state: WorkflowFailedState [2018-10-09 01:01:25,78] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. [2018-10-09 01:01:30,58] [info] Workflow polling stopped [2018-10-09 01:01:30,60] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds [2018-10-09 01:01:30,60] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds [2018-10-09 01:01:30,61] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds [2018-10-09 01:01:30,61] [info] JobExecutionTokenDispenser stopped [2018-10-09 01:01:30,61] [info] Aborting all running workflows. [2018-10-09 01:01:30,61] [info] WorkflowStoreActor stopped [2018-10-09 01:01:30,61] [info] WorkflowLogCopyRouter stopped [2018-10-09 01:01:30,61] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds [2018-10-09 01:01:30,61] [info] WorkflowManagerActor All workflows finished [2018-10-09 01:01:30,61] [info] WorkflowManagerActor stopped [2018-10-09 01:01:30,61] [info] Connection pools shut down [2018-10-09 01:01:30,61] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds [2018-10-09 01:01:30,61] [info] Shutting down JobStoreActor - Timeout = 1800 seconds [2018-10-09 01:01:30,61] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds [2018-10-09 01:01:30,61] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds [2018-10-09 01:01:30,61] [info] SubWorkflowStoreActor stopped [2018-10-09 01:01:30,61] [info] Shutting down DockerHashActor - Timeout = 1800 seconds [2018-10-09 01:01:30,61] [info] Shutting down IoProxy - Timeout = 1800 seconds [2018-10-09 01:01:30,61] [info] KvWriteActor Shutting down: 0 queued messages to process [2018-10-09 01:01:30,61] [info] CallCacheWriteActor Shutting down: 0 queued messages to process [2018-10-09 01:01:30,61] [info] WriteMetadataActor Shutting down: 0 queued messages to process [2018-10-09 01:01:30,61] [info] JobStoreActor stopped [2018-10-09 01:01:30,61] [info] CallCacheWriteActor stopped [2018-10-09 01:01:30,61] [info] DockerHashActor stopped [2018-10-09 01:01:30,62] [info] IoProxy stopped [2018-10-09 01:01:30,62] [info] ServiceRegistryActor stopped [2018-10-09 01:01:30,63] [info] Database closed [2018-10-09 01:01:30,63] [info] Stream materializer shut down Workflow ec34099b-7f45-4a33-b205-0cd6011f53f0 transitioned to state Failed [2018-10-09 01:01:30,66] [info] Automatic shutdown of the async connection [2018-10-09 01:01:30,66] [info] Gracefully shutdown sentry threads. [2018-10-09 01:01:30,66] [info] Shutdown finished. 2018-10-09 01:01:30 the mutect2 step is finished.