[2019-08-05 19:08:14,87] [info] Running with database db.url = jdbc:hsqldb:mem:e872caf4-fdbd-4167-a2a7-09949a4b2109;shutdown=false;hsqldb.tx=mvcc [2019-08-05 19:08:24,23] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 [2019-08-05 19:08:24,25] [info] [RenameWorkflowOptionsInMetadata] 100% [2019-08-05 19:08:24,33] [info] Running with database db.url = jdbc:hsqldb:mem:de4002f1-7e86-4687-a259-5f7502927119;shutdown=false;hsqldb.tx=mvcc [2019-08-05 19:08:24,77] [info] Slf4jLogger started [2019-08-05 19:08:25,09] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-8c6b3ed", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2019-08-05 19:08:25,16] [info] Metadata summary refreshing every 1 second. [2019-08-05 19:08:25,18] [warn] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf) [2019-08-05 19:08:25,19] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2019-08-05 19:08:25,20] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2019-08-05 19:08:25,20] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2019-08-05 19:08:25,26] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2019-08-05 19:08:25,55] [info] SingleWorkflowRunnerActor: Version 40 [2019-08-05 19:08:25,56] [info] SingleWorkflowRunnerActor: Submitting workflow [2019-08-05 19:08:25,62] [info] Unspecified type (Unspecified version) workflow 7d60aa8c-c853-4cbb-b320-029db4a1c502 submitted [2019-08-05 19:08:25,64] [info] SingleWorkflowRunnerActor: Workflow submitted 7d60aa8c-c853-4cbb-b320-029db4a1c502 [2019-08-05 19:08:25,64] [info] 1 new workflows fetched by cromid-8c6b3ed: 7d60aa8c-c853-4cbb-b320-029db4a1c502 [2019-08-05 19:08:25,64] [info] WorkflowManagerActor Starting workflow 7d60aa8c-c853-4cbb-b320-029db4a1c502 [2019-08-05 19:08:25,65] [info] WorkflowManagerActor Successfully started WorkflowActor-7d60aa8c-c853-4cbb-b320-029db4a1c502 [2019-08-05 19:08:25,65] [info] Retrieved 1 workflows from the WorkflowStoreActor [2019-08-05 19:08:25,66] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2019-08-05 19:08:25,78] [info] MaterializeWorkflowDescriptorActor [7d60aa8c]: Parsing workflow as WDL draft-2 [2019-08-05 19:08:26,68] [info] MaterializeWorkflowDescriptorActor [7d60aa8c]: Call-to-Backend assignments: PreProcessingForVariantDiscovery_GATK4.MarkDuplicates -> Local, PreProcessingForVariantDiscovery_GATK4.GatherBamFiles -> Local, PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports -> Local, PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator -> Local, PreProcessingForVariantDiscovery_GATK4.ApplyBQSR -> Local, PreProcessingForVariantDiscovery_GATK4.GetBwaVersion -> Local, PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment -> Local, PreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV -> Local, PreProcessingForVariantDiscovery_GATK4.SortAndFixTags -> Local, PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem -> Local [2019-08-05 19:08:29,09] [info] WorkflowExecutionActor-7d60aa8c-c853-4cbb-b320-029db4a1c502 [7d60aa8c]: Starting PreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV, PreProcessingForVariantDiscovery_GATK4.GetBwaVersion [2019-08-05 19:08:29,29] [info] Assigned new job execution tokens to the following groups: 7d60aa8c: 2 [2019-08-05 19:08:29,69] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.GetBwaVersion:NA:1]: # Not setting "set -o pipefail" here because /bwa has a rc=1 and we don't want to allow rc=1 to succeed # because the sed may also fail with that error and that is something we actually want to fail on. /home/fried255/cull0084/projects/gatk4_pipeline/bwa-0.7.17/bwa 2>&1 | \ grep -e '^Version' | \ sed 's/Version: //' [2019-08-05 19:08:29,69] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV:NA:1]: python < >(tee D06403_B.unmapped.unmerged.bwa.stderr.log >&2) \ | \ /home/fried255/cull0084/projects/gatk4_pipeline/samtools-1.9/samtools view -1 - > D06403_B.unmapped.unmerged.bam [2019-08-05 19:08:34,30] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:0:1]:  set -o pipefail set -e # set the bash variable needed for the command-line bash_ref_fasta=/scratch.global/friedlab_PREPARE_TEST/refdata/canFam3/canFam3.fa java -Dsamjdk.compression_level=5 -Xms3000m -jar /home/fried255/cull0084/projects/gatk4_pipeline/picard.jar \ SamToFastq \ INPUT=/scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/ConvertPairedFastQsToUnmappedBamWf/5e6a8724-2a09-4cd9-93f6-93f1ca4e8bc8/call-PairedFastQsToUnmappedBAM/shard-0/execution/D06403_A.unmapped.bam \ FASTQ=/dev/stdout \ INTERLEAVE=true \ NON_PF=true \ | \ /home/fried255/cull0084/projects/gatk4_pipeline/bwa-0.7.17/bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta /dev/stdin - 2> >(tee D06403_A.unmapped.unmerged.bwa.stderr.log >&2) \ | \ /home/fried255/cull0084/projects/gatk4_pipeline/samtools-1.9/samtools view -1 - > D06403_A.unmapped.unmerged.bam [2019-08-05 19:08:34,31] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:0:1]: executing: /bin/bash /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-SamToFastqAndBwaMem/shard-0/execution/script [2019-08-05 19:08:34,32] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:1:1]: executing: /bin/bash /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-SamToFastqAndBwaMem/shard-1/execution/script [2019-08-05 19:08:35,21] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:0:1]: job id: 21481 [2019-08-05 19:08:35,21] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:1:1]: job id: 21480 [2019-08-05 19:08:35,21] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:0:1]: Status change from - to WaitingForReturnCode [2019-08-05 19:08:35,21] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:1:1]: Status change from - to WaitingForReturnCode [2019-08-06 01:07:55,37] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:0:1]: Status change from WaitingForReturnCode to Done [2019-08-06 01:07:56,41] [info] WorkflowExecutionActor-7d60aa8c-c853-4cbb-b320-029db4a1c502 [7d60aa8c]: Starting PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment [2019-08-06 01:07:57,28] [info] Assigned new job execution tokens to the following groups: 7d60aa8c: 1 [2019-08-06 01:07:57,31] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:0:1]: # set the bash variable needed for the command-line bash_ref_fasta=/scratch.global/friedlab_PREPARE_TEST/refdata/canFam3/canFam3.fa /home/fried255/cull0084/projects/gatk4_pipeline/gatk-4.1.1.0/gatk --java-options "-Dsamjdk.compression_level=5 -Xms3000m" \ MergeBamAlignment \ --VALIDATION_STRINGENCY SILENT \ --EXPECTED_ORIENTATIONS FR \ --ATTRIBUTES_TO_RETAIN X0 \ --ALIGNED_BAM /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-SamToFastqAndBwaMem/shard-0/execution/D06403_A.unmapped.unmerged.bam \ --UNMAPPED_BAM /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/ConvertPairedFastQsToUnmappedBamWf/5e6a8724-2a09-4cd9-93f6-93f1ca4e8bc8/call-PairedFastQsToUnmappedBAM/shard-0/execution/D06403_A.unmapped.bam \ --OUTPUT D06403_A.unmapped.aligned.unsorted.bam \ --REFERENCE_SEQUENCE /scratch.global/friedlab_PREPARE_TEST/refdata/canFam3/canFam3.fa \ --PAIRED_RUN true \ --SORT_ORDER "unsorted" \ --IS_BISULFITE_SEQUENCE false \ --ALIGNED_READS_ONLY false \ --CLIP_ADAPTERS false \ --MAX_RECORDS_IN_RAM 2000000 \ --ADD_MATE_CIGAR true \ --MAX_INSERTIONS_OR_DELETIONS -1 \ --PRIMARY_ALIGNMENT_STRATEGY MostDistant \ --PROGRAM_RECORD_ID "bwamem" \ --PROGRAM_GROUP_VERSION "0.7.17-r1188" \ --PROGRAM_GROUP_COMMAND_LINE " mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta" \ --PROGRAM_GROUP_NAME "bwamem" \ --UNMAPPED_READ_STRATEGY COPY_TO_TAG \ --ALIGNER_PROPER_PAIR_FLAGS true \ --UNMAP_CONTAMINANT_READS true [2019-08-06 01:07:57,32] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:0:1]: executing: /bin/bash /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-0/execution/script [2019-08-06 01:08:00,23] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:0:1]: job id: 1968 [2019-08-06 01:08:00,25] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:0:1]: Status change from - to WaitingForReturnCode [2019-08-06 01:41:43,79] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:1:1]: Status change from WaitingForReturnCode to Done [2019-08-06 01:41:45,21] [info] WorkflowExecutionActor-7d60aa8c-c853-4cbb-b320-029db4a1c502 [7d60aa8c]: Starting PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment [2019-08-06 01:41:45,28] [info] Assigned new job execution tokens to the following groups: 7d60aa8c: 1 [2019-08-06 01:41:45,29] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:1:1]: # set the bash variable needed for the command-line bash_ref_fasta=/scratch.global/friedlab_PREPARE_TEST/refdata/canFam3/canFam3.fa /home/fried255/cull0084/projects/gatk4_pipeline/gatk-4.1.1.0/gatk --java-options "-Dsamjdk.compression_level=5 -Xms3000m" \ MergeBamAlignment \ --VALIDATION_STRINGENCY SILENT \ --EXPECTED_ORIENTATIONS FR \ --ATTRIBUTES_TO_RETAIN X0 \ --ALIGNED_BAM /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-SamToFastqAndBwaMem/shard-1/execution/D06403_B.unmapped.unmerged.bam \ --UNMAPPED_BAM /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/ConvertPairedFastQsToUnmappedBamWf/5e6a8724-2a09-4cd9-93f6-93f1ca4e8bc8/call-PairedFastQsToUnmappedBAM/shard-1/execution/D06403_B.unmapped.bam \ --OUTPUT D06403_B.unmapped.aligned.unsorted.bam \ --REFERENCE_SEQUENCE /scratch.global/friedlab_PREPARE_TEST/refdata/canFam3/canFam3.fa \ --PAIRED_RUN true \ --SORT_ORDER "unsorted" \ --IS_BISULFITE_SEQUENCE false \ --ALIGNED_READS_ONLY false \ --CLIP_ADAPTERS false \ --MAX_RECORDS_IN_RAM 2000000 \ --ADD_MATE_CIGAR true \ --MAX_INSERTIONS_OR_DELETIONS -1 \ --PRIMARY_ALIGNMENT_STRATEGY MostDistant \ --PROGRAM_RECORD_ID "bwamem" \ --PROGRAM_GROUP_VERSION "0.7.17-r1188" \ --PROGRAM_GROUP_COMMAND_LINE " mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta" \ --PROGRAM_GROUP_NAME "bwamem" \ --UNMAPPED_READ_STRATEGY COPY_TO_TAG \ --ALIGNER_PROPER_PAIR_FLAGS true \ --UNMAP_CONTAMINANT_READS true [2019-08-06 01:41:45,30] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:1:1]: executing: /bin/bash /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-1/execution/script [2019-08-06 01:41:50,23] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:1:1]: job id: 5624 [2019-08-06 01:41:50,23] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:1:1]: Status change from - to WaitingForReturnCode [2019-08-06 02:14:29,54] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:0:1]: Status change from WaitingForReturnCode to Done [2019-08-06 02:41:48,49] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:1:1]: Status change from WaitingForReturnCode to Done [2019-08-06 02:41:50,91] [info] WorkflowExecutionActor-7d60aa8c-c853-4cbb-b320-029db4a1c502 [7d60aa8c]: Starting PreProcessingForVariantDiscovery_GATK4.MarkDuplicates [2019-08-06 02:41:51,28] [info] Assigned new job execution tokens to the following groups: 7d60aa8c: 1 [2019-08-06 02:41:51,30] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MarkDuplicates:NA:1]: /home/fried255/cull0084/projects/gatk4_pipeline/gatk-4.1.1.0/gatk --java-options "-Dsamjdk.compression_level=5 -Xms4000m" \ MarkDuplicates \ --INPUT /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-0/execution/D06403_A.unmapped.aligned.unsorted.bam --INPUT /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-1/execution/D06403_B.unmapped.aligned.unsorted.bam \ --OUTPUT D06403.canfam3.aligned.unsorted.duplicates_marked.bam \ --METRICS_FILE D06403.canfam3.duplicate_metrics \ --VALIDATION_STRINGENCY SILENT \ --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 \ --ASSUME_SORT_ORDER "queryname" \ --CREATE_MD5_FILE true [2019-08-06 02:41:51,31] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MarkDuplicates:NA:1]: executing: /bin/bash /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MarkDuplicates/execution/script [2019-08-06 02:41:55,21] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MarkDuplicates:NA:1]: job id: 9412 [2019-08-06 02:41:55,21] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MarkDuplicates:NA:1]: Status change from - to WaitingForReturnCode [2019-08-06 13:35:54,62] [info] BackgroundConfigAsyncJobExecutionActor [7d60aa8cPreProcessingForVariantDiscovery_GATK4.MarkDuplicates:NA:1]: Status change from WaitingForReturnCode to Done [2019-08-06 13:35:55,70] [error] WorkflowManagerActor Workflow 7d60aa8c-c853-4cbb-b320-029db4a1c502 failed (during ExecutingWorkflowState): Job PreProcessingForVariantDiscovery_GATK4.MarkDuplicates:NA:1 exited with return code 250 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: /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MarkDuplicates/execution/stderr. Using GATK jar /panfs/roc/groups/0/fried255/cull0084/projects/gatk4_pipeline/gatk-4.1.1.0/gatk-package-4.1.1.0-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 -Dsamjdk.compression_level=5 -Xms4000m -jar /panfs/roc/groups/0/fried255/cull0084/projects/gatk4_pipeline/gatk-4.1.1.0/gatk-package-4.1.1.0-local.jar MarkDuplicates --INPUT /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-0/execution/D06403_A.unmapped.aligned.unsorted.bam --INPUT /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-1/execution/D06403_B.unmapped.aligned.unsorted.bam --OUTPUT D06403.canfam3.aligned.unsorted.duplicates_marked.bam --METRICS_FILE D06403.canfam3.duplicate_metrics --VALIDATION_STRINGENCY SILENT --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 --ASSUME_SORT_ORDER queryname --CREATE_MD5_FILE true Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MarkDuplicates/tmp.10e124a0 02:41:53.754 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/panfs/roc/groups/0/fried255/cull0084/projects/gatk4_pipeline/gatk-4.1.1.0/gatk-package-4.1.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Tue Aug 06 02:41:53 CDT 2019] MarkDuplicates --INPUT /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-0/execution/D06403_A.unmapped.aligned.unsorted.bam --INPUT /scratch.global/friedlab_PREPARE_TEST/mixb/D06403/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/7d60aa8c-c853-4cbb-b320-029db4a1c502/call-MergeBamAlignment/shard-1/execution/D06403_B.unmapped.aligned.unsorted.bam --OUTPUT D06403.canfam3.aligned.unsorted.duplicates_marked.bam --METRICS_FILE D06403.canfam3.duplicate_metrics --ASSUME_SORT_ORDER queryname --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 --VALIDATION_STRINGENCY SILENT --CREATE_MD5_FILE true --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false Aug 06, 2019 2:41:55 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Tue Aug 06 02:41:55 CDT 2019] Executing as cull0084@cn0046 on Linux 3.10.0-957.21.3.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.1.0 INFO 2019-08-06 02:41:55 MarkDuplicates Start of doWork freeMemory: 4778382472; totalMemory: 4817682432; maxMemory: 28631367680 INFO 2019-08-06 02:41:55 MarkDuplicates Reading input file and constructing read end information. INFO 2019-08-06 02:41:55 MarkDuplicates Will retain up to 103736839 data points before spilling to disk. INFO 2019-08-06 02:42:57 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 61s. Last read position: chr5:50,177,526 INFO 2019-08-06 02:42:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 02:43:57 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 60s. Last read position: chr22:4,048,102 INFO 2019-08-06 02:43:57 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:44:56 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 59s. Last read position: chr4:76,871,802 INFO 2019-08-06 02:44:56 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:45:56 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 60s. Last read position: chr36:18,132,146 INFO 2019-08-06 02:45:56 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:47:03 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 67s. Last read position: chr21:44,384,627 INFO 2019-08-06 02:47:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 02:48:09 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 65s. Last read position: chr1:75,345,611 INFO 2019-08-06 02:48:09 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:49:16 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 66s. Last read position: chr25:27,507,713 INFO 2019-08-06 02:49:16 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:50:21 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 65s. Last read position: chr14:17,348,642 INFO 2019-08-06 02:50:21 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:51:17 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 55s. Last read position: chr3:7,991,953 INFO 2019-08-06 02:51:17 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:52:25 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 67s. Last read position: chr30:2,795,313 INFO 2019-08-06 02:52:25 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:53:25 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 59s. Last read position: chr22:16,779,986 INFO 2019-08-06 02:53:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 02:54:26 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 61s. Last read position: chr34:6,155,967 INFO 2019-08-06 02:54:26 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:55:28 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 62s. Last read position: chr3:1,297,581 INFO 2019-08-06 02:55:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 02:56:31 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 63s. Last read position: chr3:9,572,440 INFO 2019-08-06 02:56:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 02:57:36 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:15:40s. Time for last 1,000,000: 64s. Last read position: chr14:47,529,206 INFO 2019-08-06 02:57:36 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 02:58:51 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:16:55s. Time for last 1,000,000: 75s. Last read position: chr9:32,693,279 INFO 2019-08-06 02:58:51 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:00:07 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:18:11s. Time for last 1,000,000: 75s. Last read position: chr10:46,719,266 INFO 2019-08-06 03:00:07 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:01:24 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:19:28s. Time for last 1,000,000: 77s. Last read position: chr19:4,181,626 INFO 2019-08-06 03:01:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:02:42 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:20:46s. Time for last 1,000,000: 77s. Last read position: chr2:30,584,736 INFO 2019-08-06 03:02:42 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:03:59 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:22:03s. Time for last 1,000,000: 77s. Last read position: chr23:957,673 INFO 2019-08-06 03:03:59 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:05:21 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:23:25s. Time for last 1,000,000: 81s. Last read position: chr27:14,913,618 INFO 2019-08-06 03:05:21 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:06:56 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:25:00s. Time for last 1,000,000: 95s. Last read position: chr6:24,675,939 INFO 2019-08-06 03:06:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:08:22 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:26:25s. Time for last 1,000,000: 85s. Last read position: chr14:44,270,258 INFO 2019-08-06 03:08:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:09:47 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:27:51s. Time for last 1,000,000: 85s. Last read position: chr11:35,465,368 INFO 2019-08-06 03:09:47 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:11:07 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:29:11s. Time for last 1,000,000: 80s. Last read position: chr7:48,100,920 INFO 2019-08-06 03:11:07 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:12:41 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:30:45s. Time for last 1,000,000: 93s. Last read position: chr29:40,075,227 INFO 2019-08-06 03:12:41 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:14:00 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:32:04s. Time for last 1,000,000: 78s. Last read position: chr12:23,959,557 INFO 2019-08-06 03:14:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:15:10 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:33:14s. Time for last 1,000,000: 70s. Last read position: chrX:102,370,246 INFO 2019-08-06 03:15:10 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:16:25 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:34:29s. Time for last 1,000,000: 74s. Last read position: chr4:84,688,232 INFO 2019-08-06 03:16:25 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:17:43 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:35:46s. Time for last 1,000,000: 77s. Last read position: chr25:7,932,110 INFO 2019-08-06 03:17:43 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:19:09 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:37:13s. Time for last 1,000,000: 86s. Last read position: chr23:83,315 INFO 2019-08-06 03:19:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:20:29 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:38:33s. Time for last 1,000,000: 79s. Last read position: chr19:19,595,647 INFO 2019-08-06 03:20:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:21:46 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:39:50s. Time for last 1,000,000: 76s. Last read position: chr7:35,969,210 INFO 2019-08-06 03:21:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:23:06 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:41:10s. Time for last 1,000,000: 79s. Last read position: chr28:597,469 INFO 2019-08-06 03:23:06 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:24:25 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:42:29s. Time for last 1,000,000: 78s. Last read position: chr13:48,149,550 INFO 2019-08-06 03:24:25 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:25:33 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:43:37s. Time for last 1,000,000: 68s. Last read position: chr22:41,274,853 INFO 2019-08-06 03:25:33 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:26:52 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:44:56s. Time for last 1,000,000: 79s. Last read position: chr22:21,865,097 INFO 2019-08-06 03:26:52 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:28:09 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:46:13s. Time for last 1,000,000: 76s. Last read position: chr27:8,972,973 INFO 2019-08-06 03:28:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:29:22 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:47:26s. Time for last 1,000,000: 73s. Last read position: chr33:19,196,428 INFO 2019-08-06 03:29:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:30:42 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:48:46s. Time for last 1,000,000: 79s. Last read position: chr37:14,329,380 INFO 2019-08-06 03:30:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:32:02 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:50:06s. Time for last 1,000,000: 80s. Last read position: chr13:10,446,903 INFO 2019-08-06 03:32:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:33:17 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:51:21s. Time for last 1,000,000: 74s. Last read position: chr37:7,670,706 INFO 2019-08-06 03:33:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:34:33 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:52:37s. Time for last 1,000,000: 76s. Last read position: chr30:7,855,643 INFO 2019-08-06 03:34:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:35:47 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:53:51s. Time for last 1,000,000: 73s. Last read position: chr2:2,566,960 INFO 2019-08-06 03:35:47 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:37:06 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:55:10s. Time for last 1,000,000: 79s. Last read position: chr16:25,417,296 INFO 2019-08-06 03:37:06 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:38:17 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:56:21s. Time for last 1,000,000: 71s. Last read position: chr17:36,875,574 INFO 2019-08-06 03:38:17 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:39:28 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:57:32s. Time for last 1,000,000: 70s. Last read position: chr12:35,238,708 INFO 2019-08-06 03:39:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:40:35 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:58:39s. Time for last 1,000,000: 67s. Last read position: chr38:13,574,386 INFO 2019-08-06 03:40:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:41:46 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:59:50s. Time for last 1,000,000: 71s. Last read position: chr32:8,827,715 INFO 2019-08-06 03:41:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:43:00 MarkDuplicates Read 50,000,000 records. Elapsed time: 01:01:04s. Time for last 1,000,000: 74s. Last read position: chr1:14,116,773 INFO 2019-08-06 03:43:00 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:44:12 MarkDuplicates Read 51,000,000 records. Elapsed time: 01:02:16s. Time for last 1,000,000: 72s. Last read position: chr29:1,755,711 INFO 2019-08-06 03:44:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:45:19 MarkDuplicates Read 52,000,000 records. Elapsed time: 01:03:23s. Time for last 1,000,000: 67s. Last read position: chr1:41,555,599 INFO 2019-08-06 03:45:19 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:46:26 MarkDuplicates Read 53,000,000 records. Elapsed time: 01:04:30s. Time for last 1,000,000: 66s. Last read position: chr13:48,957,459 INFO 2019-08-06 03:46:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:47:32 MarkDuplicates Read 54,000,000 records. Elapsed time: 01:05:36s. Time for last 1,000,000: 66s. Last read position: chrX:6,864,320 INFO 2019-08-06 03:47:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:48:40 MarkDuplicates Read 55,000,000 records. Elapsed time: 01:06:44s. Time for last 1,000,000: 68s. Last read position: chr38:7,492,175 INFO 2019-08-06 03:48:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:49:51 MarkDuplicates Read 56,000,000 records. Elapsed time: 01:07:55s. Time for last 1,000,000: 70s. Last read position: chr8:70,913,976 INFO 2019-08-06 03:49:51 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:51:02 MarkDuplicates Read 57,000,000 records. Elapsed time: 01:09:06s. Time for last 1,000,000: 70s. Last read position: chr21:34,231,520 INFO 2019-08-06 03:51:02 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:52:13 MarkDuplicates Read 58,000,000 records. Elapsed time: 01:10:16s. Time for last 1,000,000: 70s. Last read position: chr17:29,525,778 INFO 2019-08-06 03:52:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:53:20 MarkDuplicates Read 59,000,000 records. Elapsed time: 01:11:24s. Time for last 1,000,000: 67s. Last read position: chrX:62,190,658 INFO 2019-08-06 03:53:20 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:54:27 MarkDuplicates Read 60,000,000 records. Elapsed time: 01:12:31s. Time for last 1,000,000: 67s. Last read position: chr14:42,679,253 INFO 2019-08-06 03:54:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 03:55:31 MarkDuplicates Read 61,000,000 records. Elapsed time: 01:13:35s. Time for last 1,000,000: 64s. Last read position: chrUn_AAEX03023827:4,713 INFO 2019-08-06 03:55:31 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:56:37 MarkDuplicates Read 62,000,000 records. Elapsed time: 01:14:41s. Time for last 1,000,000: 65s. Last read position: chr9:26,171,696 INFO 2019-08-06 03:56:37 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:57:45 MarkDuplicates Read 63,000,000 records. Elapsed time: 01:15:49s. Time for last 1,000,000: 67s. Last read position: chr21:45,149,947 INFO 2019-08-06 03:57:45 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:58:50 MarkDuplicates Read 64,000,000 records. Elapsed time: 01:16:54s. Time for last 1,000,000: 65s. Last read position: chr25:11,373,077 INFO 2019-08-06 03:58:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 03:59:58 MarkDuplicates Read 65,000,000 records. Elapsed time: 01:18:02s. Time for last 1,000,000: 67s. Last read position: chrUn_AAEX03023161:470 INFO 2019-08-06 03:59:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:01:05 MarkDuplicates Read 66,000,000 records. Elapsed time: 01:19:09s. Time for last 1,000,000: 67s. Last read position: chr29:8,193,442 INFO 2019-08-06 04:01:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:02:07 MarkDuplicates Read 67,000,000 records. Elapsed time: 01:20:11s. Time for last 1,000,000: 61s. Last read position: chr22:22,885,977 INFO 2019-08-06 04:02:07 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:03:23 MarkDuplicates Read 68,000,000 records. Elapsed time: 01:21:27s. Time for last 1,000,000: 76s. Last read position: chr21:16,070,173 INFO 2019-08-06 04:03:23 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:04:28 MarkDuplicates Read 69,000,000 records. Elapsed time: 01:22:32s. Time for last 1,000,000: 65s. Last read position: chr18:50,889,403 INFO 2019-08-06 04:04:28 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:05:33 MarkDuplicates Read 70,000,000 records. Elapsed time: 01:23:37s. Time for last 1,000,000: 64s. Last read position: chr22:15,292,249 INFO 2019-08-06 04:05:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:06:37 MarkDuplicates Read 71,000,000 records. Elapsed time: 01:24:41s. Time for last 1,000,000: 64s. Last read position: chr25:9,976,964 INFO 2019-08-06 04:06:37 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:07:43 MarkDuplicates Read 72,000,000 records. Elapsed time: 01:25:47s. Time for last 1,000,000: 65s. Last read position: chr11:59,936,272 INFO 2019-08-06 04:07:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:08:44 MarkDuplicates Read 73,000,000 records. Elapsed time: 01:26:48s. Time for last 1,000,000: 60s. Last read position: chr16:18,968,890 INFO 2019-08-06 04:08:44 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:09:46 MarkDuplicates Read 74,000,000 records. Elapsed time: 01:27:50s. Time for last 1,000,000: 62s. Last read position: chr5:13,415,103 INFO 2019-08-06 04:09:46 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:10:47 MarkDuplicates Read 75,000,000 records. Elapsed time: 01:28:51s. Time for last 1,000,000: 61s. Last read position: chr16:32,880,769 INFO 2019-08-06 04:10:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:11:47 MarkDuplicates Read 76,000,000 records. Elapsed time: 01:29:51s. Time for last 1,000,000: 60s. Last read position: chr6:62,051,421 INFO 2019-08-06 04:11:47 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:12:52 MarkDuplicates Read 77,000,000 records. Elapsed time: 01:30:55s. Time for last 1,000,000: 64s. Last read position: chr3:89,862,745 INFO 2019-08-06 04:12:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:13:51 MarkDuplicates Read 78,000,000 records. Elapsed time: 01:31:55s. Time for last 1,000,000: 59s. Last read position: chr18:6,284,680 INFO 2019-08-06 04:13:51 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:14:51 MarkDuplicates Read 79,000,000 records. Elapsed time: 01:32:55s. Time for last 1,000,000: 60s. Last read position: chr29:6,026,082 INFO 2019-08-06 04:14:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:15:51 MarkDuplicates Read 80,000,000 records. Elapsed time: 01:33:55s. Time for last 1,000,000: 60s. Last read position: chr22:58,689,015 INFO 2019-08-06 04:15:51 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:16:53 MarkDuplicates Read 81,000,000 records. Elapsed time: 01:34:57s. Time for last 1,000,000: 61s. Last read position: chr11:33,621,281 INFO 2019-08-06 04:16:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:17:52 MarkDuplicates Read 82,000,000 records. Elapsed time: 01:35:56s. Time for last 1,000,000: 59s. Last read position: chr32:26,316,772 INFO 2019-08-06 04:17:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:18:53 MarkDuplicates Read 83,000,000 records. Elapsed time: 01:36:57s. Time for last 1,000,000: 60s. Last read position: chr14:44,955,519 INFO 2019-08-06 04:18:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:19:50 MarkDuplicates Read 84,000,000 records. Elapsed time: 01:37:54s. Time for last 1,000,000: 57s. Last read position: chr15:54,956,303 INFO 2019-08-06 04:19:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:20:54 MarkDuplicates Read 85,000,000 records. Elapsed time: 01:38:58s. Time for last 1,000,000: 63s. Last read position: chr32:9,271,501 INFO 2019-08-06 04:20:54 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:21:57 MarkDuplicates Read 86,000,000 records. Elapsed time: 01:40:01s. Time for last 1,000,000: 63s. Last read position: chr27:12,383,322 INFO 2019-08-06 04:21:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:22:55 MarkDuplicates Read 87,000,000 records. Elapsed time: 01:40:59s. Time for last 1,000,000: 57s. Last read position: chr36:20,896,283 INFO 2019-08-06 04:22:55 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:23:53 MarkDuplicates Read 88,000,000 records. Elapsed time: 01:41:57s. Time for last 1,000,000: 57s. Last read position: chr11:54,262,774 INFO 2019-08-06 04:23:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:24:50 MarkDuplicates Read 89,000,000 records. Elapsed time: 01:42:54s. Time for last 1,000,000: 57s. Last read position: chrX:74,130,416 INFO 2019-08-06 04:24:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:25:49 MarkDuplicates Read 90,000,000 records. Elapsed time: 01:43:53s. Time for last 1,000,000: 59s. Last read position: chr29:7,922,703 INFO 2019-08-06 04:25:49 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:26:49 MarkDuplicates Read 91,000,000 records. Elapsed time: 01:44:53s. Time for last 1,000,000: 59s. Last read position: chr22:52,173,585 INFO 2019-08-06 04:26:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:27:47 MarkDuplicates Read 92,000,000 records. Elapsed time: 01:45:50s. Time for last 1,000,000: 57s. Last read position: chr9:44,074,301 INFO 2019-08-06 04:27:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:28:46 MarkDuplicates Read 93,000,000 records. Elapsed time: 01:46:50s. Time for last 1,000,000: 59s. Last read position: chr27:3,305,664 INFO 2019-08-06 04:28:46 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:29:41 MarkDuplicates Read 94,000,000 records. Elapsed time: 01:47:45s. Time for last 1,000,000: 55s. Last read position: chr20:6,547,204 INFO 2019-08-06 04:29:41 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:30:27 MarkDuplicates Read 95,000,000 records. Elapsed time: 01:48:31s. Time for last 1,000,000: 46s. Last read position: chr15:17,368,051 INFO 2019-08-06 04:30:27 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:31:15 MarkDuplicates Read 96,000,000 records. Elapsed time: 01:49:19s. Time for last 1,000,000: 47s. Last read position: chr18:11,174,731 INFO 2019-08-06 04:31:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:32:02 MarkDuplicates Read 97,000,000 records. Elapsed time: 01:50:06s. Time for last 1,000,000: 46s. Last read position: chr15:18,040,009 INFO 2019-08-06 04:32:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:32:50 MarkDuplicates Read 98,000,000 records. Elapsed time: 01:50:54s. Time for last 1,000,000: 48s. Last read position: chrX:88,085,187 INFO 2019-08-06 04:32:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:33:34 MarkDuplicates Read 99,000,000 records. Elapsed time: 01:51:38s. Time for last 1,000,000: 44s. Last read position: chr4:38,869,347 INFO 2019-08-06 04:33:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:34:22 MarkDuplicates Read 100,000,000 records. Elapsed time: 01:52:25s. Time for last 1,000,000: 47s. Last read position: chr23:31,594,303 INFO 2019-08-06 04:34:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:35:08 MarkDuplicates Read 101,000,000 records. Elapsed time: 01:53:12s. Time for last 1,000,000: 46s. Last read position: chr34:41,322,005 INFO 2019-08-06 04:35:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:35:56 MarkDuplicates Read 102,000,000 records. Elapsed time: 01:54:00s. Time for last 1,000,000: 47s. Last read position: chr4:22,474,635 INFO 2019-08-06 04:35:56 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:36:43 MarkDuplicates Read 103,000,000 records. Elapsed time: 01:54:47s. Time for last 1,000,000: 46s. Last read position: chr24:4,696,829 INFO 2019-08-06 04:36:43 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:37:30 MarkDuplicates Read 104,000,000 records. Elapsed time: 01:55:34s. Time for last 1,000,000: 47s. Last read position: chr13:15,387,543 INFO 2019-08-06 04:37:30 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:38:18 MarkDuplicates Read 105,000,000 records. Elapsed time: 01:56:22s. Time for last 1,000,000: 48s. Last read position: chr3:46,618,856 INFO 2019-08-06 04:38:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:40:32 MarkDuplicates Read 106,000,000 records. Elapsed time: 01:58:36s. Time for last 1,000,000: 133s. Last read position: chrX:45,232,709 INFO 2019-08-06 04:40:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:41:19 MarkDuplicates Read 107,000,000 records. Elapsed time: 01:59:23s. Time for last 1,000,000: 46s. Last read position: chr21:16,999,617 INFO 2019-08-06 04:41:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:42:04 MarkDuplicates Read 108,000,000 records. Elapsed time: 02:00:08s. Time for last 1,000,000: 45s. Last read position: chr14:36,685,043 INFO 2019-08-06 04:42:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:42:49 MarkDuplicates Read 109,000,000 records. Elapsed time: 02:00:53s. Time for last 1,000,000: 44s. Last read position: chr21:1,849,953 INFO 2019-08-06 04:42:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:43:35 MarkDuplicates Read 110,000,000 records. Elapsed time: 02:01:39s. Time for last 1,000,000: 45s. Last read position: chr6:70,281,519 INFO 2019-08-06 04:43:35 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:44:21 MarkDuplicates Read 111,000,000 records. Elapsed time: 02:02:25s. Time for last 1,000,000: 46s. Last read position: chr23:29,361,558 INFO 2019-08-06 04:44:21 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:45:04 MarkDuplicates Read 112,000,000 records. Elapsed time: 02:03:08s. Time for last 1,000,000: 43s. Last read position: chr19:797,571 INFO 2019-08-06 04:45:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:45:51 MarkDuplicates Read 113,000,000 records. Elapsed time: 02:03:55s. Time for last 1,000,000: 47s. Last read position: chrUn_AAEX03024666:7,135 INFO 2019-08-06 04:45:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:46:38 MarkDuplicates Read 114,000,000 records. Elapsed time: 02:04:42s. Time for last 1,000,000: 46s. Last read position: chr29:15,126,630 INFO 2019-08-06 04:46:38 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:47:22 MarkDuplicates Read 115,000,000 records. Elapsed time: 02:05:26s. Time for last 1,000,000: 44s. Last read position: chr4:51,282,513 INFO 2019-08-06 04:47:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:48:08 MarkDuplicates Read 116,000,000 records. Elapsed time: 02:06:12s. Time for last 1,000,000: 46s. Last read position: chr6:37,888,544 INFO 2019-08-06 04:48:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:48:53 MarkDuplicates Read 117,000,000 records. Elapsed time: 02:06:57s. Time for last 1,000,000: 44s. Last read position: chr5:4,291,151 INFO 2019-08-06 04:48:53 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:49:38 MarkDuplicates Read 118,000,000 records. Elapsed time: 02:07:42s. Time for last 1,000,000: 44s. Last read position: chrUn_JH373260:303,524 INFO 2019-08-06 04:49:38 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:50:22 MarkDuplicates Read 119,000,000 records. Elapsed time: 02:08:26s. Time for last 1,000,000: 44s. Last read position: chr1:23,381,810 INFO 2019-08-06 04:50:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:51:04 MarkDuplicates Read 120,000,000 records. Elapsed time: 02:09:08s. Time for last 1,000,000: 42s. Last read position: chr37:25,460,654 INFO 2019-08-06 04:51:04 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:52:05 MarkDuplicates Read 121,000,000 records. Elapsed time: 02:10:09s. Time for last 1,000,000: 60s. Last read position: chr28:30,203,921 INFO 2019-08-06 04:52:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:52:48 MarkDuplicates Read 122,000,000 records. Elapsed time: 02:10:52s. Time for last 1,000,000: 43s. Last read position: chr3:23,212,745 INFO 2019-08-06 04:52:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:53:29 MarkDuplicates Read 123,000,000 records. Elapsed time: 02:11:33s. Time for last 1,000,000: 40s. Last read position: chr21:2,870,543 INFO 2019-08-06 04:53:29 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:54:12 MarkDuplicates Read 124,000,000 records. Elapsed time: 02:12:16s. Time for last 1,000,000: 42s. Last read position: chr26:21,187,898 INFO 2019-08-06 04:54:12 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:54:52 MarkDuplicates Read 125,000,000 records. Elapsed time: 02:12:56s. Time for last 1,000,000: 40s. Last read position: chr25:6,427,845 INFO 2019-08-06 04:54:52 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:55:37 MarkDuplicates Read 126,000,000 records. Elapsed time: 02:13:41s. Time for last 1,000,000: 45s. Last read position: chr24:43,048,002 INFO 2019-08-06 04:55:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:56:21 MarkDuplicates Read 127,000,000 records. Elapsed time: 02:14:25s. Time for last 1,000,000: 44s. Last read position: chr11:48,881,197 INFO 2019-08-06 04:56:21 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:57:10 MarkDuplicates Read 128,000,000 records. Elapsed time: 02:15:14s. Time for last 1,000,000: 48s. Last read position: chrX:68,783,600 INFO 2019-08-06 04:57:10 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 04:57:57 MarkDuplicates Read 129,000,000 records. Elapsed time: 02:16:01s. Time for last 1,000,000: 46s. Last read position: chr1:36,083,742 INFO 2019-08-06 04:57:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:58:48 MarkDuplicates Read 130,000,000 records. Elapsed time: 02:16:52s. Time for last 1,000,000: 51s. Last read position: chr32:11,926,879 INFO 2019-08-06 04:58:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 04:59:32 MarkDuplicates Read 131,000,000 records. Elapsed time: 02:17:36s. Time for last 1,000,000: 43s. Last read position: chr13:19,271,858 INFO 2019-08-06 04:59:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:00:20 MarkDuplicates Read 132,000,000 records. Elapsed time: 02:18:24s. Time for last 1,000,000: 47s. Last read position: chr36:22,291,253 INFO 2019-08-06 05:00:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:01:02 MarkDuplicates Read 133,000,000 records. Elapsed time: 02:19:06s. Time for last 1,000,000: 42s. Last read position: chr13:1,483,167 INFO 2019-08-06 05:01:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:01:44 MarkDuplicates Read 134,000,000 records. Elapsed time: 02:19:48s. Time for last 1,000,000: 42s. Last read position: chr19:12,050,374 INFO 2019-08-06 05:01:44 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:02:27 MarkDuplicates Read 135,000,000 records. Elapsed time: 02:20:31s. Time for last 1,000,000: 42s. Last read position: chr32:16,573,522 INFO 2019-08-06 05:02:27 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:03:10 MarkDuplicates Read 136,000,000 records. Elapsed time: 02:21:14s. Time for last 1,000,000: 43s. Last read position: chrX:75,286,503 INFO 2019-08-06 05:03:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:03:52 MarkDuplicates Read 137,000,000 records. Elapsed time: 02:21:56s. Time for last 1,000,000: 41s. Last read position: chr7:11,442,669 INFO 2019-08-06 05:03:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:04:37 MarkDuplicates Read 138,000,000 records. Elapsed time: 02:22:41s. Time for last 1,000,000: 45s. Last read position: chr14:39,055,503 INFO 2019-08-06 05:04:37 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:05:18 MarkDuplicates Read 139,000,000 records. Elapsed time: 02:23:22s. Time for last 1,000,000: 41s. Last read position: chr13:27,367,369 INFO 2019-08-06 05:05:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:06:00 MarkDuplicates Read 140,000,000 records. Elapsed time: 02:24:04s. Time for last 1,000,000: 42s. Last read position: chr8:22,833,212 INFO 2019-08-06 05:06:00 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:06:42 MarkDuplicates Read 141,000,000 records. Elapsed time: 02:24:46s. Time for last 1,000,000: 41s. Last read position: chr16:21,083,302 INFO 2019-08-06 05:06:42 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:07:24 MarkDuplicates Read 142,000,000 records. Elapsed time: 02:25:28s. Time for last 1,000,000: 42s. Last read position: chr26:34,274,218 INFO 2019-08-06 05:07:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:08:06 MarkDuplicates Read 143,000,000 records. Elapsed time: 02:26:10s. Time for last 1,000,000: 41s. Last read position: chr7:19,334,224 INFO 2019-08-06 05:08:06 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:08:50 MarkDuplicates Read 144,000,000 records. Elapsed time: 02:26:54s. Time for last 1,000,000: 43s. Last read position: chr8:55,298,226 INFO 2019-08-06 05:08:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:09:33 MarkDuplicates Read 145,000,000 records. Elapsed time: 02:27:37s. Time for last 1,000,000: 42s. Last read position: chr22:7,576,441 INFO 2019-08-06 05:09:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:10:17 MarkDuplicates Read 146,000,000 records. Elapsed time: 02:28:21s. Time for last 1,000,000: 44s. Last read position: chr17:52,237,522 INFO 2019-08-06 05:10:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:11:02 MarkDuplicates Read 147,000,000 records. Elapsed time: 02:29:06s. Time for last 1,000,000: 44s. Last read position: chr21:41,869,873 INFO 2019-08-06 05:11:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:11:46 MarkDuplicates Read 148,000,000 records. Elapsed time: 02:29:50s. Time for last 1,000,000: 44s. Last read position: chrX:42,266,578 INFO 2019-08-06 05:11:46 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:12:30 MarkDuplicates Read 149,000,000 records. Elapsed time: 02:30:34s. Time for last 1,000,000: 43s. Last read position: chr11:62,083,834 INFO 2019-08-06 05:12:30 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:13:13 MarkDuplicates Read 150,000,000 records. Elapsed time: 02:31:17s. Time for last 1,000,000: 43s. Last read position: chr33:6,943,055 INFO 2019-08-06 05:13:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:13:56 MarkDuplicates Read 151,000,000 records. Elapsed time: 02:32:00s. Time for last 1,000,000: 42s. Last read position: chr23:51,454,224 INFO 2019-08-06 05:13:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:14:42 MarkDuplicates Read 152,000,000 records. Elapsed time: 02:32:46s. Time for last 1,000,000: 45s. Last read position: chr27:42,987,432 INFO 2019-08-06 05:14:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:15:26 MarkDuplicates Read 153,000,000 records. Elapsed time: 02:33:30s. Time for last 1,000,000: 44s. Last read position: chr27:28,629,042 INFO 2019-08-06 05:15:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:16:10 MarkDuplicates Read 154,000,000 records. Elapsed time: 02:34:14s. Time for last 1,000,000: 44s. Last read position: chr17:6,940,314 INFO 2019-08-06 05:16:10 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:16:52 MarkDuplicates Read 155,000,000 records. Elapsed time: 02:34:56s. Time for last 1,000,000: 42s. Last read position: chr33:29,518,383 INFO 2019-08-06 05:16:52 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:17:38 MarkDuplicates Read 156,000,000 records. Elapsed time: 02:35:42s. Time for last 1,000,000: 45s. Last read position: chr14:56,962,158 INFO 2019-08-06 05:17:38 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:18:22 MarkDuplicates Read 157,000,000 records. Elapsed time: 02:36:25s. Time for last 1,000,000: 43s. Last read position: chr3:13,626,885 INFO 2019-08-06 05:18:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:19:06 MarkDuplicates Read 158,000,000 records. Elapsed time: 02:37:10s. Time for last 1,000,000: 44s. Last read position: chr23:26,651,394 INFO 2019-08-06 05:19:06 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:19:50 MarkDuplicates Read 159,000,000 records. Elapsed time: 02:37:54s. Time for last 1,000,000: 44s. Last read position: chr36:22,481,184 INFO 2019-08-06 05:19:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:20:36 MarkDuplicates Read 160,000,000 records. Elapsed time: 02:38:40s. Time for last 1,000,000: 45s. Last read position: chrUn_JH373334:27,718 INFO 2019-08-06 05:20:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:21:22 MarkDuplicates Read 161,000,000 records. Elapsed time: 02:39:26s. Time for last 1,000,000: 45s. Last read position: chr2:66,148,870 INFO 2019-08-06 05:21:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:22:08 MarkDuplicates Read 162,000,000 records. Elapsed time: 02:40:12s. Time for last 1,000,000: 46s. Last read position: chr5:67,069,066 INFO 2019-08-06 05:22:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:22:56 MarkDuplicates Read 163,000,000 records. Elapsed time: 02:41:00s. Time for last 1,000,000: 47s. Last read position: chr35:8,610,189 INFO 2019-08-06 05:22:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:23:43 MarkDuplicates Read 164,000,000 records. Elapsed time: 02:41:47s. Time for last 1,000,000: 47s. Last read position: chr13:29,139,501 INFO 2019-08-06 05:23:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:24:30 MarkDuplicates Read 165,000,000 records. Elapsed time: 02:42:34s. Time for last 1,000,000: 46s. Last read position: chr1:5,584,385 INFO 2019-08-06 05:24:30 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:25:16 MarkDuplicates Read 166,000,000 records. Elapsed time: 02:43:20s. Time for last 1,000,000: 46s. Last read position: chr27:35,415,832 INFO 2019-08-06 05:25:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:26:04 MarkDuplicates Read 167,000,000 records. Elapsed time: 02:44:08s. Time for last 1,000,000: 47s. Last read position: chr34:3,168,267 INFO 2019-08-06 05:26:04 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:26:50 MarkDuplicates Read 168,000,000 records. Elapsed time: 02:44:54s. Time for last 1,000,000: 46s. Last read position: chr34:33,031,914 INFO 2019-08-06 05:26:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:27:39 MarkDuplicates Read 169,000,000 records. Elapsed time: 02:45:43s. Time for last 1,000,000: 48s. Last read position: chr16:53,643,282 INFO 2019-08-06 05:27:39 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:28:26 MarkDuplicates Read 170,000,000 records. Elapsed time: 02:46:30s. Time for last 1,000,000: 47s. Last read position: chr1:94,860,786 INFO 2019-08-06 05:28:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:29:15 MarkDuplicates Read 171,000,000 records. Elapsed time: 02:47:19s. Time for last 1,000,000: 49s. Last read position: chr25:10,150,921 INFO 2019-08-06 05:29:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:30:04 MarkDuplicates Read 172,000,000 records. Elapsed time: 02:48:08s. Time for last 1,000,000: 48s. Last read position: chr3:16,096,724 INFO 2019-08-06 05:30:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:30:55 MarkDuplicates Read 173,000,000 records. Elapsed time: 02:48:59s. Time for last 1,000,000: 50s. Last read position: chrX:31,056,972 INFO 2019-08-06 05:30:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:31:45 MarkDuplicates Read 174,000,000 records. Elapsed time: 02:49:49s. Time for last 1,000,000: 50s. Last read position: chr9:10,692,531 INFO 2019-08-06 05:31:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:32:39 MarkDuplicates Read 175,000,000 records. Elapsed time: 02:50:43s. Time for last 1,000,000: 53s. Last read position: chr23:29,824,860 INFO 2019-08-06 05:32:39 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:33:32 MarkDuplicates Read 176,000,000 records. Elapsed time: 02:51:36s. Time for last 1,000,000: 52s. Last read position: chr30:31,105,147 INFO 2019-08-06 05:33:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:34:26 MarkDuplicates Read 177,000,000 records. Elapsed time: 02:52:30s. Time for last 1,000,000: 54s. Last read position: chr1:19,405,416 INFO 2019-08-06 05:34:26 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:35:20 MarkDuplicates Read 178,000,000 records. Elapsed time: 02:53:24s. Time for last 1,000,000: 53s. Last read position: chr30:21,142,072 INFO 2019-08-06 05:35:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:36:51 MarkDuplicates Read 179,000,000 records. Elapsed time: 02:54:54s. Time for last 1,000,000: 90s. Last read position: chr12:52,023,363 INFO 2019-08-06 05:36:51 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:38:12 MarkDuplicates Read 180,000,000 records. Elapsed time: 02:56:16s. Time for last 1,000,000: 81s. Last read position: chr25:22,880,171 INFO 2019-08-06 05:38:12 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:39:30 MarkDuplicates Read 181,000,000 records. Elapsed time: 02:57:34s. Time for last 1,000,000: 78s. Last read position: chr8:2,308,589 INFO 2019-08-06 05:39:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:41:02 MarkDuplicates Read 182,000,000 records. Elapsed time: 02:59:06s. Time for last 1,000,000: 91s. Last read position: chr8:23,898,000 INFO 2019-08-06 05:41:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:42:42 MarkDuplicates Read 183,000,000 records. Elapsed time: 03:00:46s. Time for last 1,000,000: 99s. Last read position: chr20:40,994,549 INFO 2019-08-06 05:42:42 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:43:58 MarkDuplicates Read 184,000,000 records. Elapsed time: 03:02:01s. Time for last 1,000,000: 75s. Last read position: chr18:38,252,445 INFO 2019-08-06 05:43:58 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:44:59 MarkDuplicates Read 185,000,000 records. Elapsed time: 03:03:03s. Time for last 1,000,000: 61s. Last read position: chr2:12,982,388 INFO 2019-08-06 05:44:59 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:45:58 MarkDuplicates Read 186,000,000 records. Elapsed time: 03:04:01s. Time for last 1,000,000: 58s. Last read position: chr11:19,769,050 INFO 2019-08-06 05:45:58 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:47:00 MarkDuplicates Read 187,000,000 records. Elapsed time: 03:05:03s. Time for last 1,000,000: 61s. Last read position: chr19:48,489,104 INFO 2019-08-06 05:47:00 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:48:01 MarkDuplicates Read 188,000,000 records. Elapsed time: 03:06:04s. Time for last 1,000,000: 60s. Last read position: chr27:38,624,064 INFO 2019-08-06 05:48:01 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:49:04 MarkDuplicates Read 189,000,000 records. Elapsed time: 03:07:08s. Time for last 1,000,000: 63s. Last read position: chr3:62,433,866 INFO 2019-08-06 05:49:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:50:06 MarkDuplicates Read 190,000,000 records. Elapsed time: 03:08:10s. Time for last 1,000,000: 61s. Last read position: chrX:54,625,484 INFO 2019-08-06 05:50:06 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:51:08 MarkDuplicates Read 191,000,000 records. Elapsed time: 03:09:12s. Time for last 1,000,000: 62s. Last read position: chr1:97,112,900 INFO 2019-08-06 05:51:08 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:52:13 MarkDuplicates Read 192,000,000 records. Elapsed time: 03:10:16s. Time for last 1,000,000: 64s. Last read position: chr2:61,281,659 INFO 2019-08-06 05:52:13 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:53:22 MarkDuplicates Read 193,000,000 records. Elapsed time: 03:11:26s. Time for last 1,000,000: 69s. Last read position: chr30:35,230,823 INFO 2019-08-06 05:53:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:54:21 MarkDuplicates Read 194,000,000 records. Elapsed time: 03:12:25s. Time for last 1,000,000: 59s. Last read position: chr12:16,615,989 INFO 2019-08-06 05:54:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:55:26 MarkDuplicates Read 195,000,000 records. Elapsed time: 03:13:29s. Time for last 1,000,000: 64s. Last read position: chr2:69,611,965 INFO 2019-08-06 05:55:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 05:56:28 MarkDuplicates Read 196,000,000 records. Elapsed time: 03:14:32s. Time for last 1,000,000: 62s. Last read position: chr29:11,621,694 INFO 2019-08-06 05:56:28 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:57:35 MarkDuplicates Read 197,000,000 records. Elapsed time: 03:15:39s. Time for last 1,000,000: 67s. Last read position: chr33:17,215,897 INFO 2019-08-06 05:57:35 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:58:38 MarkDuplicates Read 198,000,000 records. Elapsed time: 03:16:42s. Time for last 1,000,000: 62s. Last read position: chr27:25,446,922 INFO 2019-08-06 05:58:38 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 05:59:42 MarkDuplicates Read 199,000,000 records. Elapsed time: 03:17:46s. Time for last 1,000,000: 64s. Last read position: chr21:10,163,998 INFO 2019-08-06 05:59:42 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:00:46 MarkDuplicates Read 200,000,000 records. Elapsed time: 03:18:50s. Time for last 1,000,000: 63s. Last read position: chr15:32,571,443 INFO 2019-08-06 06:00:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:01:54 MarkDuplicates Read 201,000,000 records. Elapsed time: 03:19:58s. Time for last 1,000,000: 67s. Last read position: chr15:11,745,264 INFO 2019-08-06 06:01:54 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:03:04 MarkDuplicates Read 202,000,000 records. Elapsed time: 03:21:08s. Time for last 1,000,000: 69s. Last read position: chr7:25,876,208 INFO 2019-08-06 06:03:04 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:04:12 MarkDuplicates Read 203,000,000 records. Elapsed time: 03:22:16s. Time for last 1,000,000: 68s. Last read position: chr20:2,123,893 INFO 2019-08-06 06:04:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:05:16 MarkDuplicates Read 204,000,000 records. Elapsed time: 03:23:20s. Time for last 1,000,000: 64s. Last read position: chr18:18,036,933 INFO 2019-08-06 06:05:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:06:25 MarkDuplicates Read 205,000,000 records. Elapsed time: 03:24:29s. Time for last 1,000,000: 68s. Last read position: chr2:45,864,706 INFO 2019-08-06 06:06:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:07:33 MarkDuplicates Read 206,000,000 records. Elapsed time: 03:25:37s. Time for last 1,000,000: 67s. Last read position: chr38:11,256,237 INFO 2019-08-06 06:07:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:08:40 MarkDuplicates Read 207,000,000 records. Elapsed time: 03:26:44s. Time for last 1,000,000: 67s. Last read position: chr33:25,183,732 INFO 2019-08-06 06:08:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:09:45 MarkDuplicates Read 208,000,000 records. Elapsed time: 03:27:49s. Time for last 1,000,000: 64s. Last read position: chr34:21,401,449 INFO 2019-08-06 06:09:45 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:10:51 MarkDuplicates Read 209,000,000 records. Elapsed time: 03:28:55s. Time for last 1,000,000: 66s. Last read position: chr21:4,424,848 INFO 2019-08-06 06:10:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:12:01 MarkDuplicates Read 210,000,000 records. Elapsed time: 03:30:05s. Time for last 1,000,000: 69s. Last read position: chr21:48,373,880 INFO 2019-08-06 06:12:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:15:04 MarkDuplicates Read 211,000,000 records. Elapsed time: 03:33:08s. Time for last 1,000,000: 182s. Last read position: chr33:13,140,268 INFO 2019-08-06 06:15:04 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:18:09 MarkDuplicates Read 212,000,000 records. Elapsed time: 03:36:13s. Time for last 1,000,000: 185s. Last read position: chr15:53,004,092 INFO 2019-08-06 06:18:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:19:19 MarkDuplicates Read 213,000,000 records. Elapsed time: 03:37:23s. Time for last 1,000,000: 70s. Last read position: chrX:37,661,512 INFO 2019-08-06 06:19:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:20:32 MarkDuplicates Read 214,000,000 records. Elapsed time: 03:38:36s. Time for last 1,000,000: 72s. Last read position: chr36:28,487,865 INFO 2019-08-06 06:20:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:21:37 MarkDuplicates Read 215,000,000 records. Elapsed time: 03:39:41s. Time for last 1,000,000: 65s. Last read position: chr1:117,848,390 INFO 2019-08-06 06:21:37 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:22:30 MarkDuplicates Read 216,000,000 records. Elapsed time: 03:40:34s. Time for last 1,000,000: 52s. Last read position: chr17:46,376,890 INFO 2019-08-06 06:22:30 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:23:22 MarkDuplicates Read 217,000,000 records. Elapsed time: 03:41:26s. Time for last 1,000,000: 52s. Last read position: chr2:47,828,489 INFO 2019-08-06 06:23:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:24:14 MarkDuplicates Read 218,000,000 records. Elapsed time: 03:42:18s. Time for last 1,000,000: 52s. Last read position: chr32:7,767,858 INFO 2019-08-06 06:24:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:25:04 MarkDuplicates Read 219,000,000 records. Elapsed time: 03:43:08s. Time for last 1,000,000: 49s. Last read position: chr6:67,561,148 INFO 2019-08-06 06:25:04 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:25:56 MarkDuplicates Read 220,000,000 records. Elapsed time: 03:44:00s. Time for last 1,000,000: 52s. Last read position: chr31:27,068,841 INFO 2019-08-06 06:25:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:26:46 MarkDuplicates Read 221,000,000 records. Elapsed time: 03:44:50s. Time for last 1,000,000: 49s. Last read position: chr6:25,747,690 INFO 2019-08-06 06:26:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:27:37 MarkDuplicates Read 222,000,000 records. Elapsed time: 03:45:41s. Time for last 1,000,000: 51s. Last read position: chr14:49,068,667 INFO 2019-08-06 06:27:37 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:28:27 MarkDuplicates Read 223,000,000 records. Elapsed time: 03:46:31s. Time for last 1,000,000: 50s. Last read position: chr20:45,903,140 INFO 2019-08-06 06:28:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:29:16 MarkDuplicates Read 224,000,000 records. Elapsed time: 03:47:20s. Time for last 1,000,000: 49s. Last read position: chr36:15,391,238 INFO 2019-08-06 06:29:16 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:30:04 MarkDuplicates Read 225,000,000 records. Elapsed time: 03:48:08s. Time for last 1,000,000: 47s. Last read position: chr12:70,435,032 INFO 2019-08-06 06:30:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:30:50 MarkDuplicates Read 226,000,000 records. Elapsed time: 03:48:54s. Time for last 1,000,000: 46s. Last read position: chr15:52,178,723 INFO 2019-08-06 06:30:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:31:35 MarkDuplicates Read 227,000,000 records. Elapsed time: 03:49:39s. Time for last 1,000,000: 45s. Last read position: chr27:840,857 INFO 2019-08-06 06:31:35 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:32:22 MarkDuplicates Read 228,000,000 records. Elapsed time: 03:50:26s. Time for last 1,000,000: 46s. Last read position: chr22:22,425,372 INFO 2019-08-06 06:32:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:33:13 MarkDuplicates Read 229,000,000 records. Elapsed time: 03:51:17s. Time for last 1,000,000: 50s. Last read position: chr3:32,221,580 INFO 2019-08-06 06:33:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:34:00 MarkDuplicates Read 230,000,000 records. Elapsed time: 03:52:04s. Time for last 1,000,000: 47s. Last read position: chr3:35,019,177 INFO 2019-08-06 06:34:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:34:50 MarkDuplicates Read 231,000,000 records. Elapsed time: 03:52:54s. Time for last 1,000,000: 49s. Last read position: chr13:17,963,022 INFO 2019-08-06 06:34:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:35:40 MarkDuplicates Read 232,000,000 records. Elapsed time: 03:53:44s. Time for last 1,000,000: 50s. Last read position: chr7:65,660,090 INFO 2019-08-06 06:35:40 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:36:29 MarkDuplicates Read 233,000,000 records. Elapsed time: 03:54:33s. Time for last 1,000,000: 49s. Last read position: chr1:89,068,589 INFO 2019-08-06 06:36:29 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:37:18 MarkDuplicates Read 234,000,000 records. Elapsed time: 03:55:21s. Time for last 1,000,000: 48s. Last read position: chr13:35,338,625 INFO 2019-08-06 06:37:18 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:38:13 MarkDuplicates Read 235,000,000 records. Elapsed time: 03:56:17s. Time for last 1,000,000: 55s. Last read position: chr2:4,604,705 INFO 2019-08-06 06:38:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:39:01 MarkDuplicates Read 236,000,000 records. Elapsed time: 03:57:05s. Time for last 1,000,000: 48s. Last read position: chr13:54,951,136 INFO 2019-08-06 06:39:01 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:39:47 MarkDuplicates Read 237,000,000 records. Elapsed time: 03:57:51s. Time for last 1,000,000: 45s. Last read position: chr31:12,219,028 INFO 2019-08-06 06:39:47 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:40:35 MarkDuplicates Read 238,000,000 records. Elapsed time: 03:58:39s. Time for last 1,000,000: 47s. Last read position: chr1:49,268,074 INFO 2019-08-06 06:40:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:41:15 MarkDuplicates Read 239,000,000 records. Elapsed time: 03:59:19s. Time for last 1,000,000: 40s. Last read position: chrX:96,461,363 INFO 2019-08-06 06:41:15 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:41:58 MarkDuplicates Read 240,000,000 records. Elapsed time: 04:00:02s. Time for last 1,000,000: 42s. Last read position: chrX:79,587,879 INFO 2019-08-06 06:41:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:42:40 MarkDuplicates Read 241,000,000 records. Elapsed time: 04:00:44s. Time for last 1,000,000: 42s. Last read position: chr7:44,050,393 INFO 2019-08-06 06:42:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:43:24 MarkDuplicates Read 242,000,000 records. Elapsed time: 04:01:28s. Time for last 1,000,000: 44s. Last read position: chr29:13,737,118 INFO 2019-08-06 06:43:24 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:44:11 MarkDuplicates Read 243,000,000 records. Elapsed time: 04:02:15s. Time for last 1,000,000: 46s. Last read position: chr7:17,879,198 INFO 2019-08-06 06:44:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:44:53 MarkDuplicates Read 244,000,000 records. Elapsed time: 04:02:57s. Time for last 1,000,000: 42s. Last read position: chr3:27,209,541 INFO 2019-08-06 06:44:53 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:45:40 MarkDuplicates Read 245,000,000 records. Elapsed time: 04:03:44s. Time for last 1,000,000: 46s. Last read position: chr12:25,396,815 INFO 2019-08-06 06:45:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:46:24 MarkDuplicates Read 246,000,000 records. Elapsed time: 04:04:28s. Time for last 1,000,000: 43s. Last read position: chrUn_JH373301:27,941 INFO 2019-08-06 06:46:24 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:47:12 MarkDuplicates Read 247,000,000 records. Elapsed time: 04:05:16s. Time for last 1,000,000: 47s. Last read position: chr9:40,825,907 INFO 2019-08-06 06:47:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:47:59 MarkDuplicates Read 248,000,000 records. Elapsed time: 04:06:03s. Time for last 1,000,000: 47s. Last read position: chr9:19,971,326 INFO 2019-08-06 06:47:59 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:48:49 MarkDuplicates Read 249,000,000 records. Elapsed time: 04:06:53s. Time for last 1,000,000: 49s. Last read position: chr17:29,969,493 INFO 2019-08-06 06:48:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:49:34 MarkDuplicates Read 250,000,000 records. Elapsed time: 04:07:38s. Time for last 1,000,000: 44s. Last read position: chr29:26,481,999 INFO 2019-08-06 06:49:34 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:50:19 MarkDuplicates Read 251,000,000 records. Elapsed time: 04:08:23s. Time for last 1,000,000: 45s. Last read position: chr27:21,416,598 INFO 2019-08-06 06:50:19 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:51:02 MarkDuplicates Read 252,000,000 records. Elapsed time: 04:09:06s. Time for last 1,000,000: 42s. Last read position: chrUn_JH373255:374,963 INFO 2019-08-06 06:51:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:51:46 MarkDuplicates Read 253,000,000 records. Elapsed time: 04:09:50s. Time for last 1,000,000: 43s. Last read position: chr7:35,073,899 INFO 2019-08-06 06:51:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:52:31 MarkDuplicates Read 254,000,000 records. Elapsed time: 04:10:35s. Time for last 1,000,000: 44s. Last read position: chr33:3,636,474 INFO 2019-08-06 06:52:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:53:15 MarkDuplicates Read 255,000,000 records. Elapsed time: 04:11:19s. Time for last 1,000,000: 44s. Last read position: chr33:20,942,312 INFO 2019-08-06 06:53:15 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:54:01 MarkDuplicates Read 256,000,000 records. Elapsed time: 04:12:05s. Time for last 1,000,000: 46s. Last read position: chr17:8,587,539 INFO 2019-08-06 06:54:01 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:54:45 MarkDuplicates Read 257,000,000 records. Elapsed time: 04:12:49s. Time for last 1,000,000: 43s. Last read position: chr5:38,497,898 INFO 2019-08-06 06:54:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:55:28 MarkDuplicates Read 258,000,000 records. Elapsed time: 04:13:32s. Time for last 1,000,000: 43s. Last read position: chr12:29,470,461 INFO 2019-08-06 06:55:28 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:56:12 MarkDuplicates Read 259,000,000 records. Elapsed time: 04:14:16s. Time for last 1,000,000: 43s. Last read position: chr5:12,004,987 INFO 2019-08-06 06:56:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:57:10 MarkDuplicates Read 260,000,000 records. Elapsed time: 04:15:13s. Time for last 1,000,000: 57s. Last read position: chr4:71,292,873 INFO 2019-08-06 06:57:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 06:57:55 MarkDuplicates Read 261,000,000 records. Elapsed time: 04:15:59s. Time for last 1,000,000: 45s. Last read position: chr15:4,399,192 INFO 2019-08-06 06:57:55 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:58:40 MarkDuplicates Read 262,000,000 records. Elapsed time: 04:16:44s. Time for last 1,000,000: 44s. Last read position: chr1:30,764,728 INFO 2019-08-06 06:58:40 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 06:59:23 MarkDuplicates Read 263,000,000 records. Elapsed time: 04:17:27s. Time for last 1,000,000: 43s. Last read position: chr11:2,270,552 INFO 2019-08-06 06:59:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:00:08 MarkDuplicates Read 264,000,000 records. Elapsed time: 04:18:12s. Time for last 1,000,000: 44s. Last read position: chr7:25,141,341 INFO 2019-08-06 07:00:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:00:50 MarkDuplicates Read 265,000,000 records. Elapsed time: 04:18:54s. Time for last 1,000,000: 41s. Last read position: chrUn_AAEX03025815:1,251 INFO 2019-08-06 07:00:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:01:32 MarkDuplicates Read 266,000,000 records. Elapsed time: 04:19:36s. Time for last 1,000,000: 41s. Last read position: chr13:51,308,460 INFO 2019-08-06 07:01:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:02:16 MarkDuplicates Read 267,000,000 records. Elapsed time: 04:20:20s. Time for last 1,000,000: 43s. Last read position: chr33:26,487,346 INFO 2019-08-06 07:02:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:03:01 MarkDuplicates Read 268,000,000 records. Elapsed time: 04:21:05s. Time for last 1,000,000: 44s. Last read position: chr13:60,322,591 INFO 2019-08-06 07:03:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:03:45 MarkDuplicates Read 269,000,000 records. Elapsed time: 04:21:49s. Time for last 1,000,000: 44s. Last read position: chr7:70,715,129 INFO 2019-08-06 07:03:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:04:27 MarkDuplicates Read 270,000,000 records. Elapsed time: 04:22:31s. Time for last 1,000,000: 42s. Last read position: chr15:55,564,282 INFO 2019-08-06 07:04:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:05:12 MarkDuplicates Read 271,000,000 records. Elapsed time: 04:23:16s. Time for last 1,000,000: 44s. Last read position: chr8:38,359,334 INFO 2019-08-06 07:05:12 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:05:55 MarkDuplicates Read 272,000,000 records. Elapsed time: 04:23:59s. Time for last 1,000,000: 42s. Last read position: chr6:39,870,959 INFO 2019-08-06 07:05:55 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:06:37 MarkDuplicates Read 273,000,000 records. Elapsed time: 04:24:41s. Time for last 1,000,000: 42s. Last read position: chr19:32,596,742 INFO 2019-08-06 07:06:37 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:07:22 MarkDuplicates Read 274,000,000 records. Elapsed time: 04:25:26s. Time for last 1,000,000: 44s. Last read position: chr6:29,551,294 INFO 2019-08-06 07:07:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:08:07 MarkDuplicates Read 275,000,000 records. Elapsed time: 04:26:11s. Time for last 1,000,000: 45s. Last read position: chrUn_JH373456:9,378 INFO 2019-08-06 07:08:07 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:08:50 MarkDuplicates Read 276,000,000 records. Elapsed time: 04:26:54s. Time for last 1,000,000: 42s. Last read position: chr18:11,986,413 INFO 2019-08-06 07:08:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:09:36 MarkDuplicates Read 277,000,000 records. Elapsed time: 04:27:40s. Time for last 1,000,000: 45s. Last read position: chr23:17,248,890 INFO 2019-08-06 07:09:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:10:18 MarkDuplicates Read 278,000,000 records. Elapsed time: 04:28:22s. Time for last 1,000,000: 41s. Last read position: chr18:4,409,988 INFO 2019-08-06 07:10:18 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:11:01 MarkDuplicates Read 279,000,000 records. Elapsed time: 04:29:05s. Time for last 1,000,000: 43s. Last read position: chrUn_AAEX03019241:25,090 INFO 2019-08-06 07:11:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:11:47 MarkDuplicates Read 280,000,000 records. Elapsed time: 04:29:51s. Time for last 1,000,000: 46s. Last read position: chr3:38,169,211 INFO 2019-08-06 07:11:47 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:12:32 MarkDuplicates Read 281,000,000 records. Elapsed time: 04:30:36s. Time for last 1,000,000: 44s. Last read position: chr16:45,668,627 INFO 2019-08-06 07:12:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:13:17 MarkDuplicates Read 282,000,000 records. Elapsed time: 04:31:21s. Time for last 1,000,000: 44s. Last read position: chr23:24,653,797 INFO 2019-08-06 07:13:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:14:00 MarkDuplicates Read 283,000,000 records. Elapsed time: 04:32:04s. Time for last 1,000,000: 43s. Last read position: chr21:5,857,663 INFO 2019-08-06 07:14:00 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:14:45 MarkDuplicates Read 284,000,000 records. Elapsed time: 04:32:49s. Time for last 1,000,000: 44s. Last read position: chr38:7,500,761 INFO 2019-08-06 07:14:45 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:15:29 MarkDuplicates Read 285,000,000 records. Elapsed time: 04:33:33s. Time for last 1,000,000: 43s. Last read position: chr6:23,684,613 INFO 2019-08-06 07:15:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:16:16 MarkDuplicates Read 286,000,000 records. Elapsed time: 04:34:19s. Time for last 1,000,000: 46s. Last read position: chr28:5,391,423 INFO 2019-08-06 07:16:16 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:16:58 MarkDuplicates Read 287,000,000 records. Elapsed time: 04:35:02s. Time for last 1,000,000: 42s. Last read position: chr4:46,244,917 INFO 2019-08-06 07:16:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:17:50 MarkDuplicates Read 288,000,000 records. Elapsed time: 04:35:54s. Time for last 1,000,000: 51s. Last read position: chr7:70,453,156 INFO 2019-08-06 07:17:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:18:35 MarkDuplicates Read 289,000,000 records. Elapsed time: 04:36:39s. Time for last 1,000,000: 44s. Last read position: chr27:22,086,091 INFO 2019-08-06 07:18:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:19:21 MarkDuplicates Read 290,000,000 records. Elapsed time: 04:37:25s. Time for last 1,000,000: 46s. Last read position: chr20:5,339,959 INFO 2019-08-06 07:19:21 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:20:08 MarkDuplicates Read 291,000,000 records. Elapsed time: 04:38:12s. Time for last 1,000,000: 46s. Last read position: chr30:19,221,603 INFO 2019-08-06 07:20:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:20:57 MarkDuplicates Read 292,000,000 records. Elapsed time: 04:39:01s. Time for last 1,000,000: 48s. Last read position: chr22:47,068,998 INFO 2019-08-06 07:20:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:21:43 MarkDuplicates Read 293,000,000 records. Elapsed time: 04:39:47s. Time for last 1,000,000: 46s. Last read position: chr24:28,346,417 INFO 2019-08-06 07:21:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:22:31 MarkDuplicates Read 294,000,000 records. Elapsed time: 04:40:35s. Time for last 1,000,000: 47s. Last read position: */* INFO 2019-08-06 07:22:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:23:18 MarkDuplicates Read 295,000,000 records. Elapsed time: 04:41:22s. Time for last 1,000,000: 47s. Last read position: chr10:17,601,336 INFO 2019-08-06 07:23:18 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:24:01 MarkDuplicates Read 296,000,000 records. Elapsed time: 04:42:05s. Time for last 1,000,000: 42s. Last read position: chr19:8,682,398 INFO 2019-08-06 07:24:01 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:24:49 MarkDuplicates Read 297,000,000 records. Elapsed time: 04:42:53s. Time for last 1,000,000: 48s. Last read position: chr6:56,961,595 INFO 2019-08-06 07:24:49 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:25:32 MarkDuplicates Read 298,000,000 records. Elapsed time: 04:43:36s. Time for last 1,000,000: 43s. Last read position: chr13:43,823,533 INFO 2019-08-06 07:25:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:26:19 MarkDuplicates Read 299,000,000 records. Elapsed time: 04:44:23s. Time for last 1,000,000: 46s. Last read position: chr5:44,825,134 INFO 2019-08-06 07:26:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:27:03 MarkDuplicates Read 300,000,000 records. Elapsed time: 04:45:07s. Time for last 1,000,000: 44s. Last read position: chr9:44,538,226 INFO 2019-08-06 07:27:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:27:50 MarkDuplicates Read 301,000,000 records. Elapsed time: 04:45:54s. Time for last 1,000,000: 47s. Last read position: chr3:56,992,198 INFO 2019-08-06 07:27:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:28:35 MarkDuplicates Read 302,000,000 records. Elapsed time: 04:46:39s. Time for last 1,000,000: 44s. Last read position: chr3:72,424,273 INFO 2019-08-06 07:28:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:29:18 MarkDuplicates Read 303,000,000 records. Elapsed time: 04:47:22s. Time for last 1,000,000: 43s. Last read position: chr22:16,728,174 INFO 2019-08-06 07:29:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:30:04 MarkDuplicates Read 304,000,000 records. Elapsed time: 04:48:08s. Time for last 1,000,000: 45s. Last read position: chr28:37,928,073 INFO 2019-08-06 07:30:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:30:50 MarkDuplicates Read 305,000,000 records. Elapsed time: 04:48:54s. Time for last 1,000,000: 45s. Last read position: chr11:18,183,125 INFO 2019-08-06 07:30:50 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:31:31 MarkDuplicates Read 306,000,000 records. Elapsed time: 04:49:35s. Time for last 1,000,000: 41s. Last read position: chr36:19,202,510 INFO 2019-08-06 07:31:31 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:32:13 MarkDuplicates Read 307,000,000 records. Elapsed time: 04:50:17s. Time for last 1,000,000: 42s. Last read position: chr25:6,075,993 INFO 2019-08-06 07:32:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:32:57 MarkDuplicates Read 308,000,000 records. Elapsed time: 04:51:01s. Time for last 1,000,000: 43s. Last read position: chr1:6,245,981 INFO 2019-08-06 07:32:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:33:42 MarkDuplicates Read 309,000,000 records. Elapsed time: 04:51:46s. Time for last 1,000,000: 44s. Last read position: chr13:33,367,131 INFO 2019-08-06 07:33:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:34:27 MarkDuplicates Read 310,000,000 records. Elapsed time: 04:52:31s. Time for last 1,000,000: 45s. Last read position: chr37:28,496,267 INFO 2019-08-06 07:34:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:35:13 MarkDuplicates Read 311,000,000 records. Elapsed time: 04:53:17s. Time for last 1,000,000: 45s. Last read position: chr21:44,031,416 INFO 2019-08-06 07:35:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:36:03 MarkDuplicates Read 312,000,000 records. Elapsed time: 04:54:07s. Time for last 1,000,000: 50s. Last read position: chr1:91,522,988 INFO 2019-08-06 07:36:03 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:36:50 MarkDuplicates Read 313,000,000 records. Elapsed time: 04:54:54s. Time for last 1,000,000: 47s. Last read position: chr26:26,367,559 INFO 2019-08-06 07:36:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:37:38 MarkDuplicates Read 314,000,000 records. Elapsed time: 04:55:42s. Time for last 1,000,000: 47s. Last read position: chr22:5,863,956 INFO 2019-08-06 07:37:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:38:28 MarkDuplicates Read 315,000,000 records. Elapsed time: 04:56:32s. Time for last 1,000,000: 50s. Last read position: chr29:18,235,023 INFO 2019-08-06 07:38:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:40:44 MarkDuplicates Read 316,000,000 records. Elapsed time: 04:58:48s. Time for last 1,000,000: 136s. Last read position: chr24:13,592,935 INFO 2019-08-06 07:40:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:41:33 MarkDuplicates Read 317,000,000 records. Elapsed time: 04:59:37s. Time for last 1,000,000: 48s. Last read position: chr25:22,091,886 INFO 2019-08-06 07:41:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:42:16 MarkDuplicates Read 318,000,000 records. Elapsed time: 05:00:20s. Time for last 1,000,000: 43s. Last read position: chr5:9,321,367 INFO 2019-08-06 07:42:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:43:01 MarkDuplicates Read 319,000,000 records. Elapsed time: 05:01:05s. Time for last 1,000,000: 44s. Last read position: chrX:17,973,777 INFO 2019-08-06 07:43:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:43:47 MarkDuplicates Read 320,000,000 records. Elapsed time: 05:01:51s. Time for last 1,000,000: 45s. Last read position: chr15:50,380,622 INFO 2019-08-06 07:43:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:44:31 MarkDuplicates Read 321,000,000 records. Elapsed time: 05:02:35s. Time for last 1,000,000: 44s. Last read position: chr26:26,236,467 INFO 2019-08-06 07:44:31 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:45:17 MarkDuplicates Read 322,000,000 records. Elapsed time: 05:03:21s. Time for last 1,000,000: 45s. Last read position: chr9:26,419,779 INFO 2019-08-06 07:45:17 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:46:02 MarkDuplicates Read 323,000,000 records. Elapsed time: 05:04:06s. Time for last 1,000,000: 45s. Last read position: chr10:8,208,499 INFO 2019-08-06 07:46:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:46:46 MarkDuplicates Read 324,000,000 records. Elapsed time: 05:04:50s. Time for last 1,000,000: 44s. Last read position: chr32:509,210 INFO 2019-08-06 07:46:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:47:31 MarkDuplicates Read 325,000,000 records. Elapsed time: 05:05:35s. Time for last 1,000,000: 44s. Last read position: chr14:25,021,787 INFO 2019-08-06 07:47:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:48:17 MarkDuplicates Read 326,000,000 records. Elapsed time: 05:06:21s. Time for last 1,000,000: 45s. Last read position: chr8:54,513,241 INFO 2019-08-06 07:48:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:49:00 MarkDuplicates Read 327,000,000 records. Elapsed time: 05:07:04s. Time for last 1,000,000: 43s. Last read position: chr9:29,369,903 INFO 2019-08-06 07:49:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:49:41 MarkDuplicates Read 328,000,000 records. Elapsed time: 05:07:45s. Time for last 1,000,000: 40s. Last read position: chr7:45,650,188 INFO 2019-08-06 07:49:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:50:25 MarkDuplicates Read 329,000,000 records. Elapsed time: 05:08:29s. Time for last 1,000,000: 43s. Last read position: chr36:5,033,147 INFO 2019-08-06 07:50:25 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:51:06 MarkDuplicates Read 330,000,000 records. Elapsed time: 05:09:10s. Time for last 1,000,000: 41s. Last read position: chrUn_JH373253:403,365 INFO 2019-08-06 07:51:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:51:51 MarkDuplicates Read 331,000,000 records. Elapsed time: 05:09:55s. Time for last 1,000,000: 44s. Last read position: chr25:25,656,744 INFO 2019-08-06 07:51:51 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:52:32 MarkDuplicates Read 332,000,000 records. Elapsed time: 05:10:36s. Time for last 1,000,000: 41s. Last read position: chr8:27,480,296 INFO 2019-08-06 07:52:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:53:17 MarkDuplicates Read 333,000,000 records. Elapsed time: 05:11:21s. Time for last 1,000,000: 45s. Last read position: chr1:76,064,342 INFO 2019-08-06 07:53:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:53:58 MarkDuplicates Read 334,000,000 records. Elapsed time: 05:12:02s. Time for last 1,000,000: 41s. Last read position: chr17:30,560,036 INFO 2019-08-06 07:53:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:54:42 MarkDuplicates Read 335,000,000 records. Elapsed time: 05:12:46s. Time for last 1,000,000: 44s. Last read position: chrX:26,652,942 INFO 2019-08-06 07:54:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:55:23 MarkDuplicates Read 336,000,000 records. Elapsed time: 05:13:27s. Time for last 1,000,000: 41s. Last read position: chr33:19,415,239 INFO 2019-08-06 07:55:23 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:56:05 MarkDuplicates Read 337,000,000 records. Elapsed time: 05:14:09s. Time for last 1,000,000: 41s. Last read position: chr12:36,702,521 INFO 2019-08-06 07:56:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:56:49 MarkDuplicates Read 338,000,000 records. Elapsed time: 05:14:53s. Time for last 1,000,000: 44s. Last read position: chr14:37,039,488 INFO 2019-08-06 07:56:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:57:31 MarkDuplicates Read 339,000,000 records. Elapsed time: 05:15:35s. Time for last 1,000,000: 42s. Last read position: chr8:36,885,137 INFO 2019-08-06 07:57:31 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:58:16 MarkDuplicates Read 340,000,000 records. Elapsed time: 05:16:20s. Time for last 1,000,000: 44s. Last read position: chr14:54,982,082 INFO 2019-08-06 07:58:16 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 07:59:01 MarkDuplicates Read 341,000,000 records. Elapsed time: 05:17:05s. Time for last 1,000,000: 44s. Last read position: chrX:81,991,079 INFO 2019-08-06 07:59:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 07:59:48 MarkDuplicates Read 342,000,000 records. Elapsed time: 05:17:52s. Time for last 1,000,000: 47s. Last read position: chr2:48,068,514 INFO 2019-08-06 07:59:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:00:33 MarkDuplicates Read 343,000,000 records. Elapsed time: 05:18:37s. Time for last 1,000,000: 44s. Last read position: chrX:102,738,288 INFO 2019-08-06 08:00:33 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:01:24 MarkDuplicates Read 344,000,000 records. Elapsed time: 05:19:27s. Time for last 1,000,000: 50s. Last read position: chr17:58,891,733 INFO 2019-08-06 08:01:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:02:14 MarkDuplicates Read 345,000,000 records. Elapsed time: 05:20:18s. Time for last 1,000,000: 50s. Last read position: chr30:17,778,062 INFO 2019-08-06 08:02:14 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:03:06 MarkDuplicates Read 346,000,000 records. Elapsed time: 05:21:10s. Time for last 1,000,000: 51s. Last read position: chr1:111,279,014 INFO 2019-08-06 08:03:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:03:56 MarkDuplicates Read 347,000,000 records. Elapsed time: 05:22:00s. Time for last 1,000,000: 50s. Last read position: chr13:14,715,541 INFO 2019-08-06 08:03:56 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:04:46 MarkDuplicates Read 348,000,000 records. Elapsed time: 05:22:50s. Time for last 1,000,000: 50s. Last read position: chr1:99,990,086 INFO 2019-08-06 08:04:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:05:33 MarkDuplicates Read 349,000,000 records. Elapsed time: 05:23:37s. Time for last 1,000,000: 47s. Last read position: chrUn_AAEX03025158:5,697 INFO 2019-08-06 08:05:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:06:23 MarkDuplicates Read 350,000,000 records. Elapsed time: 05:24:27s. Time for last 1,000,000: 49s. Last read position: chr16:48,141,815 INFO 2019-08-06 08:06:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:07:12 MarkDuplicates Read 351,000,000 records. Elapsed time: 05:25:16s. Time for last 1,000,000: 49s. Last read position: chr15:18,195,767 INFO 2019-08-06 08:07:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:08:01 MarkDuplicates Read 352,000,000 records. Elapsed time: 05:26:05s. Time for last 1,000,000: 49s. Last read position: chr1:86,789,232 INFO 2019-08-06 08:08:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:08:50 MarkDuplicates Read 353,000,000 records. Elapsed time: 05:26:54s. Time for last 1,000,000: 49s. Last read position: chr22:40,144,051 INFO 2019-08-06 08:08:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:09:37 MarkDuplicates Read 354,000,000 records. Elapsed time: 05:27:41s. Time for last 1,000,000: 46s. Last read position: chr14:5,110,911 INFO 2019-08-06 08:09:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:10:24 MarkDuplicates Read 355,000,000 records. Elapsed time: 05:28:28s. Time for last 1,000,000: 47s. Last read position: chr21:46,973,063 INFO 2019-08-06 08:10:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:11:10 MarkDuplicates Read 356,000,000 records. Elapsed time: 05:29:14s. Time for last 1,000,000: 46s. Last read position: chrX:31,836,042 INFO 2019-08-06 08:11:10 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:11:57 MarkDuplicates Read 357,000,000 records. Elapsed time: 05:30:01s. Time for last 1,000,000: 46s. Last read position: chr1:5,079,209 INFO 2019-08-06 08:11:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:12:42 MarkDuplicates Read 358,000,000 records. Elapsed time: 05:30:46s. Time for last 1,000,000: 44s. Last read position: chr10:2,940,090 INFO 2019-08-06 08:12:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:13:27 MarkDuplicates Read 359,000,000 records. Elapsed time: 05:31:31s. Time for last 1,000,000: 44s. Last read position: chr20:10,362,898 INFO 2019-08-06 08:13:27 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:14:12 MarkDuplicates Read 360,000,000 records. Elapsed time: 05:32:16s. Time for last 1,000,000: 45s. Last read position: chr23:24,372,752 INFO 2019-08-06 08:14:12 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:14:56 MarkDuplicates Read 361,000,000 records. Elapsed time: 05:33:00s. Time for last 1,000,000: 44s. Last read position: chrX:9,548,901 INFO 2019-08-06 08:14:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:15:42 MarkDuplicates Read 362,000,000 records. Elapsed time: 05:33:46s. Time for last 1,000,000: 45s. Last read position: chr31:742,944 INFO 2019-08-06 08:15:42 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:16:25 MarkDuplicates Read 363,000,000 records. Elapsed time: 05:34:29s. Time for last 1,000,000: 43s. Last read position: chr32:23,788,347 INFO 2019-08-06 08:16:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:17:08 MarkDuplicates Read 364,000,000 records. Elapsed time: 05:35:12s. Time for last 1,000,000: 43s. Last read position: chr21:31,840,870 INFO 2019-08-06 08:17:08 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:17:54 MarkDuplicates Read 365,000,000 records. Elapsed time: 05:35:58s. Time for last 1,000,000: 45s. Last read position: chr3:47,909,249 INFO 2019-08-06 08:17:54 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:18:44 MarkDuplicates Read 366,000,000 records. Elapsed time: 05:36:48s. Time for last 1,000,000: 49s. Last read position: chr14:14,090,789 INFO 2019-08-06 08:18:44 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:19:33 MarkDuplicates Read 367,000,000 records. Elapsed time: 05:37:37s. Time for last 1,000,000: 49s. Last read position: chr2:38,677,665 INFO 2019-08-06 08:19:33 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:20:22 MarkDuplicates Read 368,000,000 records. Elapsed time: 05:38:26s. Time for last 1,000,000: 48s. Last read position: chr30:345,583 INFO 2019-08-06 08:20:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:21:06 MarkDuplicates Read 369,000,000 records. Elapsed time: 05:39:10s. Time for last 1,000,000: 44s. Last read position: chr7:22,573,234 INFO 2019-08-06 08:21:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:21:52 MarkDuplicates Read 370,000,000 records. Elapsed time: 05:39:56s. Time for last 1,000,000: 45s. Last read position: chr28:20,506,267 INFO 2019-08-06 08:21:52 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:22:37 MarkDuplicates Read 371,000,000 records. Elapsed time: 05:40:41s. Time for last 1,000,000: 45s. Last read position: chr25:5,338,086 INFO 2019-08-06 08:22:37 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:23:23 MarkDuplicates Read 372,000,000 records. Elapsed time: 05:41:26s. Time for last 1,000,000: 45s. Last read position: chrX:33,482,473 INFO 2019-08-06 08:23:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:24:10 MarkDuplicates Read 373,000,000 records. Elapsed time: 05:42:14s. Time for last 1,000,000: 47s. Last read position: chr5:86,021,634 INFO 2019-08-06 08:24:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:24:52 MarkDuplicates Read 374,000,000 records. Elapsed time: 05:42:56s. Time for last 1,000,000: 41s. Last read position: chr9:28,866,533 INFO 2019-08-06 08:24:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:25:36 MarkDuplicates Read 375,000,000 records. Elapsed time: 05:43:40s. Time for last 1,000,000: 44s. Last read position: chrUn_JH373271:81,111 INFO 2019-08-06 08:25:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:26:19 MarkDuplicates Read 376,000,000 records. Elapsed time: 05:44:23s. Time for last 1,000,000: 42s. Last read position: chr12:6,818,465 INFO 2019-08-06 08:26:19 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:27:03 MarkDuplicates Read 377,000,000 records. Elapsed time: 05:45:07s. Time for last 1,000,000: 43s. Last read position: chrX:81,415,911 INFO 2019-08-06 08:27:03 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:27:47 MarkDuplicates Read 378,000,000 records. Elapsed time: 05:45:51s. Time for last 1,000,000: 44s. Last read position: chr8:4,333,372 INFO 2019-08-06 08:27:47 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:28:31 MarkDuplicates Read 379,000,000 records. Elapsed time: 05:46:35s. Time for last 1,000,000: 43s. Last read position: chr6:66,762,519 INFO 2019-08-06 08:28:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:29:15 MarkDuplicates Read 380,000,000 records. Elapsed time: 05:47:19s. Time for last 1,000,000: 43s. Last read position: chr12:49,715,663 INFO 2019-08-06 08:29:15 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:30:30 MarkDuplicates Read 381,000,000 records. Elapsed time: 05:48:34s. Time for last 1,000,000: 74s. Last read position: chr3:56,598,636 INFO 2019-08-06 08:30:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:31:15 MarkDuplicates Read 382,000,000 records. Elapsed time: 05:49:19s. Time for last 1,000,000: 45s. Last read position: chr16:4,656,773 INFO 2019-08-06 08:31:15 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:31:59 MarkDuplicates Read 383,000,000 records. Elapsed time: 05:50:03s. Time for last 1,000,000: 43s. Last read position: chr11:36,384,944 INFO 2019-08-06 08:31:59 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:32:44 MarkDuplicates Read 384,000,000 records. Elapsed time: 05:50:48s. Time for last 1,000,000: 45s. Last read position: chr18:13,786,816 INFO 2019-08-06 08:32:44 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:33:29 MarkDuplicates Read 385,000,000 records. Elapsed time: 05:51:33s. Time for last 1,000,000: 44s. Last read position: chr38:5,641,191 INFO 2019-08-06 08:33:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:34:13 MarkDuplicates Read 386,000,000 records. Elapsed time: 05:52:17s. Time for last 1,000,000: 44s. Last read position: chr28:2,221,469 INFO 2019-08-06 08:34:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:34:57 MarkDuplicates Read 387,000,000 records. Elapsed time: 05:53:01s. Time for last 1,000,000: 43s. Last read position: chr2:16,777,389 INFO 2019-08-06 08:34:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:35:44 MarkDuplicates Read 388,000,000 records. Elapsed time: 05:53:48s. Time for last 1,000,000: 46s. Last read position: chr28:4,365,933 INFO 2019-08-06 08:35:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:36:37 MarkDuplicates Read 389,000,000 records. Elapsed time: 05:54:40s. Time for last 1,000,000: 52s. Last read position: chr18:13,493,575 INFO 2019-08-06 08:36:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:37:26 MarkDuplicates Read 390,000,000 records. Elapsed time: 05:55:30s. Time for last 1,000,000: 49s. Last read position: chr5:7,683,962 INFO 2019-08-06 08:37:26 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:38:14 MarkDuplicates Read 391,000,000 records. Elapsed time: 05:56:17s. Time for last 1,000,000: 47s. Last read position: chr3:20,362,338 INFO 2019-08-06 08:38:14 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:39:04 MarkDuplicates Read 392,000,000 records. Elapsed time: 05:57:08s. Time for last 1,000,000: 50s. Last read position: chr17:20,186,915 INFO 2019-08-06 08:39:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:39:49 MarkDuplicates Read 393,000,000 records. Elapsed time: 05:57:53s. Time for last 1,000,000: 44s. Last read position: chr1:17,482,425 INFO 2019-08-06 08:39:49 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:40:39 MarkDuplicates Read 394,000,000 records. Elapsed time: 05:58:43s. Time for last 1,000,000: 49s. Last read position: chr6:36,809,150 INFO 2019-08-06 08:40:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:41:22 MarkDuplicates Read 395,000,000 records. Elapsed time: 05:59:26s. Time for last 1,000,000: 43s. Last read position: chrUn_JH373420:41,589 INFO 2019-08-06 08:41:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:42:04 MarkDuplicates Read 396,000,000 records. Elapsed time: 06:00:08s. Time for last 1,000,000: 41s. Last read position: chr16:7,294,015 INFO 2019-08-06 08:42:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:42:50 MarkDuplicates Read 397,000,000 records. Elapsed time: 06:00:54s. Time for last 1,000,000: 45s. Last read position: chr21:44,615,822 INFO 2019-08-06 08:42:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:43:36 MarkDuplicates Read 398,000,000 records. Elapsed time: 06:01:40s. Time for last 1,000,000: 45s. Last read position: chr7:61,445,107 INFO 2019-08-06 08:43:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:44:42 MarkDuplicates Read 399,000,000 records. Elapsed time: 06:02:46s. Time for last 1,000,000: 65s. Last read position: chr16:45,718,454 INFO 2019-08-06 08:44:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:45:25 MarkDuplicates Read 400,000,000 records. Elapsed time: 06:03:29s. Time for last 1,000,000: 43s. Last read position: chr4:83,563,218 INFO 2019-08-06 08:45:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:46:16 MarkDuplicates Read 401,000,000 records. Elapsed time: 06:04:20s. Time for last 1,000,000: 50s. Last read position: chr22:18,525,336 INFO 2019-08-06 08:46:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:47:01 MarkDuplicates Read 402,000,000 records. Elapsed time: 06:05:05s. Time for last 1,000,000: 45s. Last read position: chr6:43,080,458 INFO 2019-08-06 08:47:01 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:47:51 MarkDuplicates Read 403,000,000 records. Elapsed time: 06:05:55s. Time for last 1,000,000: 49s. Last read position: chr1:59,072,626 INFO 2019-08-06 08:47:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:48:37 MarkDuplicates Read 404,000,000 records. Elapsed time: 06:06:41s. Time for last 1,000,000: 45s. Last read position: chr12:40,971,337 INFO 2019-08-06 08:48:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:49:21 MarkDuplicates Read 405,000,000 records. Elapsed time: 06:07:25s. Time for last 1,000,000: 44s. Last read position: chr16:40,392,262 INFO 2019-08-06 08:49:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:50:11 MarkDuplicates Read 406,000,000 records. Elapsed time: 06:08:15s. Time for last 1,000,000: 50s. Last read position: chr9:25,300,527 INFO 2019-08-06 08:50:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:50:54 MarkDuplicates Read 407,000,000 records. Elapsed time: 06:08:58s. Time for last 1,000,000: 42s. Last read position: chr20:30,159,674 INFO 2019-08-06 08:50:54 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:51:40 MarkDuplicates Read 408,000,000 records. Elapsed time: 06:09:44s. Time for last 1,000,000: 46s. Last read position: chr16:46,095,271 INFO 2019-08-06 08:51:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:52:32 MarkDuplicates Read 409,000,000 records. Elapsed time: 06:10:36s. Time for last 1,000,000: 51s. Last read position: chr21:45,950,081 INFO 2019-08-06 08:52:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:53:22 MarkDuplicates Read 410,000,000 records. Elapsed time: 06:11:26s. Time for last 1,000,000: 50s. Last read position: chr38:1,183,907 INFO 2019-08-06 08:53:22 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:54:07 MarkDuplicates Read 411,000,000 records. Elapsed time: 06:12:11s. Time for last 1,000,000: 45s. Last read position: chr16:10,484,528 INFO 2019-08-06 08:54:07 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:54:54 MarkDuplicates Read 412,000,000 records. Elapsed time: 06:12:58s. Time for last 1,000,000: 46s. Last read position: chr31:487,987 INFO 2019-08-06 08:54:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:55:40 MarkDuplicates Read 413,000,000 records. Elapsed time: 06:13:44s. Time for last 1,000,000: 45s. Last read position: chr1:9,667,889 INFO 2019-08-06 08:55:40 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:56:26 MarkDuplicates Read 414,000,000 records. Elapsed time: 06:14:30s. Time for last 1,000,000: 45s. Last read position: chr7:22,473,387 INFO 2019-08-06 08:56:26 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:57:13 MarkDuplicates Read 415,000,000 records. Elapsed time: 06:15:17s. Time for last 1,000,000: 47s. Last read position: chr7:27,084,526 INFO 2019-08-06 08:57:13 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:57:58 MarkDuplicates Read 416,000,000 records. Elapsed time: 06:16:02s. Time for last 1,000,000: 44s. Last read position: chr1:90,489,748 INFO 2019-08-06 08:57:58 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 08:58:44 MarkDuplicates Read 417,000,000 records. Elapsed time: 06:16:48s. Time for last 1,000,000: 46s. Last read position: chr5:51,989,288 INFO 2019-08-06 08:58:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 08:59:30 MarkDuplicates Read 418,000,000 records. Elapsed time: 06:17:34s. Time for last 1,000,000: 45s. Last read position: chr12:53,340,481 INFO 2019-08-06 08:59:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:00:17 MarkDuplicates Read 419,000,000 records. Elapsed time: 06:18:21s. Time for last 1,000,000: 47s. Last read position: chr7:22,843,699 INFO 2019-08-06 09:00:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:01:02 MarkDuplicates Read 420,000,000 records. Elapsed time: 06:19:06s. Time for last 1,000,000: 44s. Last read position: chr24:34,903,998 INFO 2019-08-06 09:01:02 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:03:12 MarkDuplicates Read 421,000,000 records. Elapsed time: 06:21:16s. Time for last 1,000,000: 130s. Last read position: chr34:14,843,775 INFO 2019-08-06 09:03:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:03:59 MarkDuplicates Read 422,000,000 records. Elapsed time: 06:22:02s. Time for last 1,000,000: 46s. Last read position: chr32:25,771,905 INFO 2019-08-06 09:03:59 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:06:25 MarkDuplicates Read 423,000,000 records. Elapsed time: 06:24:29s. Time for last 1,000,000: 146s. Last read position: chr12:45,231,792 INFO 2019-08-06 09:06:25 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:07:12 MarkDuplicates Read 424,000,000 records. Elapsed time: 06:25:16s. Time for last 1,000,000: 46s. Last read position: chr14:30,412,852 INFO 2019-08-06 09:07:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:07:58 MarkDuplicates Read 425,000,000 records. Elapsed time: 06:26:01s. Time for last 1,000,000: 45s. Last read position: chr16:56,782,303 INFO 2019-08-06 09:07:58 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:08:44 MarkDuplicates Read 426,000,000 records. Elapsed time: 06:26:48s. Time for last 1,000,000: 46s. Last read position: chrUn_AAEX03025169:4,139 INFO 2019-08-06 09:08:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:09:29 MarkDuplicates Read 427,000,000 records. Elapsed time: 06:27:33s. Time for last 1,000,000: 44s. Last read position: chrUn_JH373970:11,545 INFO 2019-08-06 09:09:29 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:10:14 MarkDuplicates Read 428,000,000 records. Elapsed time: 06:28:18s. Time for last 1,000,000: 45s. Last read position: chr7:52,767,329 INFO 2019-08-06 09:10:14 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:11:01 MarkDuplicates Read 429,000,000 records. Elapsed time: 06:29:05s. Time for last 1,000,000: 47s. Last read position: chr22:20,187,889 INFO 2019-08-06 09:11:01 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:11:47 MarkDuplicates Read 430,000,000 records. Elapsed time: 06:29:51s. Time for last 1,000,000: 45s. Last read position: chr29:21,962,603 INFO 2019-08-06 09:11:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:12:32 MarkDuplicates Read 431,000,000 records. Elapsed time: 06:30:36s. Time for last 1,000,000: 45s. Last read position: chr4:15,376,945 INFO 2019-08-06 09:12:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:13:18 MarkDuplicates Read 432,000,000 records. Elapsed time: 06:31:21s. Time for last 1,000,000: 45s. Last read position: chr1:51,477,355 INFO 2019-08-06 09:13:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:14:05 MarkDuplicates Read 433,000,000 records. Elapsed time: 06:32:09s. Time for last 1,000,000: 47s. Last read position: chr17:39,368,576 INFO 2019-08-06 09:14:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:14:52 MarkDuplicates Read 434,000,000 records. Elapsed time: 06:32:56s. Time for last 1,000,000: 46s. Last read position: chr25:12,090,227 INFO 2019-08-06 09:14:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:15:38 MarkDuplicates Read 435,000,000 records. Elapsed time: 06:33:42s. Time for last 1,000,000: 46s. Last read position: chr7:38,084,295 INFO 2019-08-06 09:15:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:16:24 MarkDuplicates Read 436,000,000 records. Elapsed time: 06:34:28s. Time for last 1,000,000: 46s. Last read position: chr4:83,861,901 INFO 2019-08-06 09:16:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:17:11 MarkDuplicates Read 437,000,000 records. Elapsed time: 06:35:15s. Time for last 1,000,000: 47s. Last read position: chr17:11,788,541 INFO 2019-08-06 09:17:11 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:17:59 MarkDuplicates Read 438,000,000 records. Elapsed time: 06:36:03s. Time for last 1,000,000: 47s. Last read position: chr19:52,710,015 INFO 2019-08-06 09:17:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:18:45 MarkDuplicates Read 439,000,000 records. Elapsed time: 06:36:49s. Time for last 1,000,000: 46s. Last read position: chr29:17,865,114 INFO 2019-08-06 09:18:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:19:30 MarkDuplicates Read 440,000,000 records. Elapsed time: 06:37:34s. Time for last 1,000,000: 44s. Last read position: chr25:38,455,485 INFO 2019-08-06 09:19:30 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:20:14 MarkDuplicates Read 441,000,000 records. Elapsed time: 06:38:18s. Time for last 1,000,000: 43s. Last read position: chr10:32,815,589 INFO 2019-08-06 09:20:14 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:20:55 MarkDuplicates Read 442,000,000 records. Elapsed time: 06:38:59s. Time for last 1,000,000: 41s. Last read position: chr5:34,359,040 INFO 2019-08-06 09:20:55 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:21:43 MarkDuplicates Read 443,000,000 records. Elapsed time: 06:39:47s. Time for last 1,000,000: 48s. Last read position: chr25:38,910,864 INFO 2019-08-06 09:21:43 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:22:27 MarkDuplicates Read 444,000,000 records. Elapsed time: 06:40:31s. Time for last 1,000,000: 43s. Last read position: chr11:2,651,858 INFO 2019-08-06 09:22:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:23:13 MarkDuplicates Read 445,000,000 records. Elapsed time: 06:41:17s. Time for last 1,000,000: 45s. Last read position: chr1:39,352,449 INFO 2019-08-06 09:23:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:23:57 MarkDuplicates Read 446,000,000 records. Elapsed time: 06:42:01s. Time for last 1,000,000: 43s. Last read position: chr11:32,201,436 INFO 2019-08-06 09:23:57 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:24:46 MarkDuplicates Read 447,000,000 records. Elapsed time: 06:42:50s. Time for last 1,000,000: 49s. Last read position: chr1:59,953,436 INFO 2019-08-06 09:24:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:25:41 MarkDuplicates Read 448,000,000 records. Elapsed time: 06:43:45s. Time for last 1,000,000: 55s. Last read position: chr28:40,404,680 INFO 2019-08-06 09:25:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:26:44 MarkDuplicates Read 449,000,000 records. Elapsed time: 06:44:48s. Time for last 1,000,000: 63s. Last read position: chr7:20,544,758 INFO 2019-08-06 09:26:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:27:47 MarkDuplicates Read 450,000,000 records. Elapsed time: 06:45:51s. Time for last 1,000,000: 62s. Last read position: chr4:49,022,944 INFO 2019-08-06 09:27:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:28:44 MarkDuplicates Read 451,000,000 records. Elapsed time: 06:46:48s. Time for last 1,000,000: 57s. Last read position: chr16:8,652,382 INFO 2019-08-06 09:28:44 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:29:52 MarkDuplicates Read 452,000,000 records. Elapsed time: 06:47:56s. Time for last 1,000,000: 67s. Last read position: chr19:773,449 INFO 2019-08-06 09:29:52 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:30:58 MarkDuplicates Read 453,000,000 records. Elapsed time: 06:49:02s. Time for last 1,000,000: 66s. Last read position: chr33:25,091,888 INFO 2019-08-06 09:30:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:32:12 MarkDuplicates Read 454,000,000 records. Elapsed time: 06:50:15s. Time for last 1,000,000: 73s. Last read position: chr5:21,627,342 INFO 2019-08-06 09:32:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:33:21 MarkDuplicates Read 455,000,000 records. Elapsed time: 06:51:25s. Time for last 1,000,000: 69s. Last read position: chr17:12,669,941 INFO 2019-08-06 09:33:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:34:35 MarkDuplicates Read 456,000,000 records. Elapsed time: 06:52:39s. Time for last 1,000,000: 74s. Last read position: chr12:28,495,856 INFO 2019-08-06 09:34:35 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:35:49 MarkDuplicates Read 457,000,000 records. Elapsed time: 06:53:53s. Time for last 1,000,000: 73s. Last read position: chr6:22,088,366 INFO 2019-08-06 09:35:49 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:37:02 MarkDuplicates Read 458,000,000 records. Elapsed time: 06:55:06s. Time for last 1,000,000: 73s. Last read position: chr10:60,360,579 INFO 2019-08-06 09:37:02 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:38:15 MarkDuplicates Read 459,000,000 records. Elapsed time: 06:56:19s. Time for last 1,000,000: 73s. Last read position: chr8:7,468,634 INFO 2019-08-06 09:38:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:39:32 MarkDuplicates Read 460,000,000 records. Elapsed time: 06:57:36s. Time for last 1,000,000: 77s. Last read position: chr22:39,154,785 INFO 2019-08-06 09:39:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:40:52 MarkDuplicates Read 461,000,000 records. Elapsed time: 06:58:56s. Time for last 1,000,000: 79s. Last read position: chrUn_AAEX03020105:26,992 INFO 2019-08-06 09:40:52 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:42:08 MarkDuplicates Read 462,000,000 records. Elapsed time: 07:00:12s. Time for last 1,000,000: 76s. Last read position: chr18:41,534,420 INFO 2019-08-06 09:42:08 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:43:26 MarkDuplicates Read 463,000,000 records. Elapsed time: 07:01:30s. Time for last 1,000,000: 78s. Last read position: chr6:7,052,297 INFO 2019-08-06 09:43:26 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:44:47 MarkDuplicates Read 464,000,000 records. Elapsed time: 07:02:51s. Time for last 1,000,000: 80s. Last read position: chr16:46,810,757 INFO 2019-08-06 09:44:47 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:46:10 MarkDuplicates Read 465,000,000 records. Elapsed time: 07:04:14s. Time for last 1,000,000: 83s. Last read position: chr20:26,248,706 INFO 2019-08-06 09:46:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:47:29 MarkDuplicates Read 466,000,000 records. Elapsed time: 07:05:33s. Time for last 1,000,000: 78s. Last read position: chr10:4,710,104 INFO 2019-08-06 09:47:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:48:55 MarkDuplicates Read 467,000,000 records. Elapsed time: 07:06:59s. Time for last 1,000,000: 86s. Last read position: chr21:5,743,701 INFO 2019-08-06 09:48:55 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:50:17 MarkDuplicates Read 468,000,000 records. Elapsed time: 07:08:21s. Time for last 1,000,000: 82s. Last read position: chr13:23,102,576 INFO 2019-08-06 09:50:17 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:51:40 MarkDuplicates Read 469,000,000 records. Elapsed time: 07:09:44s. Time for last 1,000,000: 82s. Last read position: chr32:5,996,143 INFO 2019-08-06 09:51:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:53:07 MarkDuplicates Read 470,000,000 records. Elapsed time: 07:11:11s. Time for last 1,000,000: 87s. Last read position: chr15:12,120,985 INFO 2019-08-06 09:53:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:54:33 MarkDuplicates Read 471,000,000 records. Elapsed time: 07:12:37s. Time for last 1,000,000: 86s. Last read position: chr26:6,322,910 INFO 2019-08-06 09:54:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:55:58 MarkDuplicates Read 472,000,000 records. Elapsed time: 07:14:02s. Time for last 1,000,000: 85s. Last read position: chr15:60,930,509 INFO 2019-08-06 09:55:58 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:57:20 MarkDuplicates Read 473,000,000 records. Elapsed time: 07:15:24s. Time for last 1,000,000: 82s. Last read position: chr22:14,937,303 INFO 2019-08-06 09:57:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 09:58:38 MarkDuplicates Read 474,000,000 records. Elapsed time: 07:16:42s. Time for last 1,000,000: 77s. Last read position: chr5:55,966,716 INFO 2019-08-06 09:58:38 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 09:59:49 MarkDuplicates Read 475,000,000 records. Elapsed time: 07:17:53s. Time for last 1,000,000: 70s. Last read position: chr14:36,926,062 INFO 2019-08-06 09:59:49 MarkDuplicates Tracking 1 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:01:55 MarkDuplicates Read 476,000,000 records. Elapsed time: 07:19:59s. Time for last 1,000,000: 126s. Last read position: chr37:18,677,362 INFO 2019-08-06 10:01:55 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:03:15 MarkDuplicates Read 477,000,000 records. Elapsed time: 07:21:19s. Time for last 1,000,000: 79s. Last read position: chr13:63,115,451 INFO 2019-08-06 10:03:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:04:40 MarkDuplicates Read 478,000,000 records. Elapsed time: 07:22:44s. Time for last 1,000,000: 85s. Last read position: chr3:49,882,934 INFO 2019-08-06 10:04:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:06:11 MarkDuplicates Read 479,000,000 records. Elapsed time: 07:24:15s. Time for last 1,000,000: 90s. Last read position: chrUn_AAEX03025530:3,986 INFO 2019-08-06 10:06:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:07:32 MarkDuplicates Read 480,000,000 records. Elapsed time: 07:25:36s. Time for last 1,000,000: 81s. Last read position: chr5:50,502,989 INFO 2019-08-06 10:07:32 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:08:58 MarkDuplicates Read 481,000,000 records. Elapsed time: 07:27:02s. Time for last 1,000,000: 85s. Last read position: chr8:9,973,279 INFO 2019-08-06 10:08:58 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:10:19 MarkDuplicates Read 482,000,000 records. Elapsed time: 07:28:23s. Time for last 1,000,000: 81s. Last read position: chr31:25,670,893 INFO 2019-08-06 10:10:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:11:42 MarkDuplicates Read 483,000,000 records. Elapsed time: 07:29:46s. Time for last 1,000,000: 83s. Last read position: chr25:16,921,275 INFO 2019-08-06 10:11:42 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:13:05 MarkDuplicates Read 484,000,000 records. Elapsed time: 07:31:09s. Time for last 1,000,000: 82s. Last read position: chr1:12,318,000 INFO 2019-08-06 10:13:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:14:31 MarkDuplicates Read 485,000,000 records. Elapsed time: 07:32:35s. Time for last 1,000,000: 86s. Last read position: chr32:2,302,262 INFO 2019-08-06 10:14:31 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:16:03 MarkDuplicates Read 486,000,000 records. Elapsed time: 07:34:06s. Time for last 1,000,000: 91s. Last read position: chr19:41,057,886 INFO 2019-08-06 10:16:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:17:30 MarkDuplicates Read 487,000,000 records. Elapsed time: 07:35:34s. Time for last 1,000,000: 87s. Last read position: chr36:8,221,621 INFO 2019-08-06 10:17:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:18:56 MarkDuplicates Read 488,000,000 records. Elapsed time: 07:37:00s. Time for last 1,000,000: 85s. Last read position: chr23:38,088,671 INFO 2019-08-06 10:18:56 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:20:25 MarkDuplicates Read 489,000,000 records. Elapsed time: 07:38:29s. Time for last 1,000,000: 89s. Last read position: chr2:23,421,962 INFO 2019-08-06 10:20:25 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:21:51 MarkDuplicates Read 490,000,000 records. Elapsed time: 07:39:55s. Time for last 1,000,000: 86s. Last read position: chr12:17,978,549 INFO 2019-08-06 10:21:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:23:12 MarkDuplicates Read 491,000,000 records. Elapsed time: 07:41:16s. Time for last 1,000,000: 80s. Last read position: chr12:72,265,301 INFO 2019-08-06 10:23:12 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:24:20 MarkDuplicates Read 492,000,000 records. Elapsed time: 07:42:24s. Time for last 1,000,000: 68s. Last read position: chr33:1,005,925 INFO 2019-08-06 10:24:20 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:25:36 MarkDuplicates Read 493,000,000 records. Elapsed time: 07:43:40s. Time for last 1,000,000: 75s. Last read position: chr37:1,801,312 INFO 2019-08-06 10:25:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:26:53 MarkDuplicates Read 494,000,000 records. Elapsed time: 07:44:57s. Time for last 1,000,000: 77s. Last read position: chr8:27,211,702 INFO 2019-08-06 10:26:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:28:10 MarkDuplicates Read 495,000,000 records. Elapsed time: 07:46:14s. Time for last 1,000,000: 77s. Last read position: chr2:50,016,005 INFO 2019-08-06 10:28:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:29:31 MarkDuplicates Read 496,000,000 records. Elapsed time: 07:47:35s. Time for last 1,000,000: 81s. Last read position: chr1:41,179,682 INFO 2019-08-06 10:29:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:30:42 MarkDuplicates Read 497,000,000 records. Elapsed time: 07:48:46s. Time for last 1,000,000: 70s. Last read position: chrX:54,246,205 INFO 2019-08-06 10:30:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 10:32:02 MarkDuplicates Read 498,000,000 records. Elapsed time: 07:50:06s. Time for last 1,000,000: 79s. Last read position: chrUn_JH373457:1,696 INFO 2019-08-06 10:32:02 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:33:18 MarkDuplicates Read 499,000,000 records. Elapsed time: 07:51:22s. Time for last 1,000,000: 76s. Last read position: chr32:33,066,418 INFO 2019-08-06 10:33:18 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:40:40 MarkDuplicates Read 500,000,000 records. Elapsed time: 07:58:44s. Time for last 1,000,000: 441s. Last read position: chr37:18,829,626 INFO 2019-08-06 10:40:40 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:49:35 MarkDuplicates Read 501,000,000 records. Elapsed time: 08:07:39s. Time for last 1,000,000: 534s. Last read position: chrX:9,419,866 INFO 2019-08-06 10:49:35 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 10:57:29 MarkDuplicates Read 502,000,000 records. Elapsed time: 08:15:33s. Time for last 1,000,000: 474s. Last read position: chr35:19,414,081 INFO 2019-08-06 10:57:29 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 11:04:48 MarkDuplicates Read 503,000,000 records. Elapsed time: 08:22:52s. Time for last 1,000,000: 438s. Last read position: chr36:7,365,396 INFO 2019-08-06 11:04:48 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 11:12:26 MarkDuplicates Read 504,000,000 records. Elapsed time: 08:30:30s. Time for last 1,000,000: 458s. Last read position: chr9:54,384,960 INFO 2019-08-06 11:12:26 MarkDuplicates Tracking 1 as yet unmatched pairs. 1 records in RAM. INFO 2019-08-06 11:19:30 MarkDuplicates Read 505,000,000 records. Elapsed time: 08:37:34s. Time for last 1,000,000: 423s. Last read position: chr3:3,464,061 INFO 2019-08-06 11:19:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 11:26:11 MarkDuplicates Read 506,000,000 records. Elapsed time: 08:44:15s. Time for last 1,000,000: 401s. Last read position: chr1:102,335,300 INFO 2019-08-06 11:26:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2019-08-06 11:30:43 MarkDuplicates Read 506691598 records. 0 pairs never matched. INFO 2019-08-06 11:32:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 28694895504; totalMemory: 28858384384; maxMemory: 28858384384 INFO 2019-08-06 11:32:16 MarkDuplicates Will retain up to 901824512 duplicate indices before spilling to disk. INFO 2019-08-06 11:32:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2019-08-06 11:32:19 SortingCollection Creating merging iterator from 3 files WARNING 2019-08-06 11:32:21 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2019-08-06 11:34:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2019-08-06 11:34:33 SortingCollection Creating merging iterator from 5 files WARNING 2019-08-06 11:34:35 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2019-08-06 11:38:06 MarkDuplicates Sorting list of duplicate records. INFO 2019-08-06 11:38:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 19570729224; totalMemory: 26959937536; maxMemory: 28631367680 INFO 2019-08-06 11:38:10 MarkDuplicates Marking 14513620 records as duplicates. INFO 2019-08-06 11:38:10 MarkDuplicates Found 10216414 optical duplicate clusters. INFO 2019-08-06 11:38:13 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2019-08-06 11:38:13 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2019-08-06 11:40:30 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:17s. Time for last 10,000,000: 137s. Last read position: chr30:2,795,313 INFO 2019-08-06 11:42:48 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:04:34s. Time for last 10,000,000: 137s. Last read position: chr23:957,673 INFO 2019-08-06 11:45:04 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:06:50s. Time for last 10,000,000: 135s. Last read position: chr25:7,932,110 INFO 2019-08-06 11:47:18 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:09:04s. Time for last 10,000,000: 134s. Last read position: chr37:14,329,380 INFO 2019-08-06 11:49:31 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:11:18s. Time for last 10,000,000: 133s. Last read position: chr1:14,116,773 INFO 2019-08-06 11:51:46 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:13:33s. Time for last 10,000,000: 135s. Last read position: chr14:42,679,253 INFO 2019-08-06 11:54:02 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:15:48s. Time for last 10,000,000: 135s. Last read position: chr22:15,292,249 INFO 2019-08-06 11:56:19 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:18:05s. Time for last 10,000,000: 137s. Last read position: chr22:58,689,015 INFO 2019-08-06 11:58:35 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:20:22s. Time for last 10,000,000: 136s. Last read position: chr29:7,922,703 INFO 2019-08-06 12:00:49 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:22:36s. Time for last 10,000,000: 134s. Last read position: chr23:31,594,303 INFO 2019-08-06 12:03:02 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:24:49s. Time for last 10,000,000: 133s. Last read position: chr6:70,281,519 INFO 2019-08-06 12:05:16 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:27:03s. Time for last 10,000,000: 133s. Last read position: chr37:25,460,654 INFO 2019-08-06 12:07:34 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:29:21s. Time for last 10,000,000: 138s. Last read position: chr32:11,926,879 INFO 2019-08-06 12:09:55 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:31:42s. Time for last 10,000,000: 140s. Last read position: chr8:22,833,212 INFO 2019-08-06 12:12:14 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:34:01s. Time for last 10,000,000: 138s. Last read position: chr33:6,943,055 INFO 2019-08-06 12:14:29 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:36:15s. Time for last 10,000,000: 134s. Last read position: chrUn_JH373334:27,718 INFO 2019-08-06 12:16:44 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:38:30s. Time for last 10,000,000: 135s. Last read position: chr1:94,860,786 INFO 2019-08-06 12:19:01 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:40:48s. Time for last 10,000,000: 137s. Last read position: chr25:22,880,171 INFO 2019-08-06 12:21:17 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:43:04s. Time for last 10,000,000: 136s. Last read position: chrX:54,625,484 INFO 2019-08-06 12:23:37 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:45:24s. Time for last 10,000,000: 139s. Last read position: chr15:32,571,443 INFO 2019-08-06 12:25:56 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:47:43s. Time for last 10,000,000: 138s. Last read position: chr21:48,373,880 INFO 2019-08-06 12:28:10 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:49:57s. Time for last 10,000,000: 133s. Last read position: chr31:27,068,841 INFO 2019-08-06 12:30:24 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:52:11s. Time for last 10,000,000: 134s. Last read position: chr3:35,019,177 INFO 2019-08-06 12:32:42 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:54:29s. Time for last 10,000,000: 137s. Last read position: chrX:79,587,879 INFO 2019-08-06 12:34:56 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:56:43s. Time for last 10,000,000: 134s. Last read position: chr29:26,481,999 INFO 2019-08-06 12:37:13 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:59:00s. Time for last 10,000,000: 137s. Last read position: chr4:71,292,873 INFO 2019-08-06 12:39:30 MarkDuplicates Written 270,000,000 records. Elapsed time: 01:01:16s. Time for last 10,000,000: 136s. Last read position: chr15:55,564,282 INFO 2019-08-06 12:41:45 MarkDuplicates Written 280,000,000 records. Elapsed time: 01:03:32s. Time for last 10,000,000: 135s. Last read position: chr3:38,169,211 INFO 2019-08-06 12:43:59 MarkDuplicates Written 290,000,000 records. Elapsed time: 01:05:46s. Time for last 10,000,000: 133s. Last read position: chr20:5,339,959 INFO 2019-08-06 12:46:13 MarkDuplicates Written 300,000,000 records. Elapsed time: 01:08:00s. Time for last 10,000,000: 134s. Last read position: chr9:44,538,226 INFO 2019-08-06 12:48:29 MarkDuplicates Written 310,000,000 records. Elapsed time: 01:10:16s. Time for last 10,000,000: 136s. Last read position: chr37:28,496,267 INFO 2019-08-06 12:50:45 MarkDuplicates Written 320,000,000 records. Elapsed time: 01:12:31s. Time for last 10,000,000: 135s. Last read position: chr15:50,380,622 INFO 2019-08-06 12:53:01 MarkDuplicates Written 330,000,000 records. Elapsed time: 01:14:48s. Time for last 10,000,000: 136s. Last read position: chrUn_JH373253:403,365 INFO 2019-08-06 12:55:17 MarkDuplicates Written 340,000,000 records. Elapsed time: 01:17:04s. Time for last 10,000,000: 136s. Last read position: chr14:54,982,082 INFO 2019-08-06 12:57:31 MarkDuplicates Written 350,000,000 records. Elapsed time: 01:19:18s. Time for last 10,000,000: 133s. Last read position: chr16:48,141,815 INFO 2019-08-06 12:59:44 MarkDuplicates Written 360,000,000 records. Elapsed time: 01:21:30s. Time for last 10,000,000: 132s. Last read position: chr23:24,372,752 INFO 2019-08-06 13:01:59 MarkDuplicates Written 370,000,000 records. Elapsed time: 01:23:46s. Time for last 10,000,000: 135s. Last read position: chr28:20,506,267 INFO 2019-08-06 13:04:16 MarkDuplicates Written 380,000,000 records. Elapsed time: 01:26:03s. Time for last 10,000,000: 137s. Last read position: chr12:49,715,663 INFO 2019-08-06 13:06:34 MarkDuplicates Written 390,000,000 records. Elapsed time: 01:28:21s. Time for last 10,000,000: 137s. Last read position: chr5:7,683,962 INFO 2019-08-06 13:08:54 MarkDuplicates Written 400,000,000 records. Elapsed time: 01:30:40s. Time for last 10,000,000: 139s. Last read position: chr4:83,563,218 INFO 2019-08-06 13:11:11 MarkDuplicates Written 410,000,000 records. Elapsed time: 01:32:58s. Time for last 10,000,000: 137s. Last read position: chr38:1,183,907 INFO 2019-08-06 13:13:25 MarkDuplicates Written 420,000,000 records. Elapsed time: 01:35:12s. Time for last 10,000,000: 134s. Last read position: chr24:34,903,998 INFO 2019-08-06 13:15:41 MarkDuplicates Written 430,000,000 records. Elapsed time: 01:37:28s. Time for last 10,000,000: 136s. Last read position: chr29:21,962,603 INFO 2019-08-06 13:17:56 MarkDuplicates Written 440,000,000 records. Elapsed time: 01:39:42s. Time for last 10,000,000: 134s. Last read position: chr25:38,455,485 INFO 2019-08-06 13:20:13 MarkDuplicates Written 450,000,000 records. Elapsed time: 01:41:59s. Time for last 10,000,000: 136s. Last read position: chr4:49,022,944 INFO 2019-08-06 13:22:32 MarkDuplicates Written 460,000,000 records. Elapsed time: 01:44:19s. Time for last 10,000,000: 139s. Last read position: chr22:39,154,785 INFO 2019-08-06 13:24:51 MarkDuplicates Written 470,000,000 records. Elapsed time: 01:46:37s. Time for last 10,000,000: 138s. Last read position: chr15:12,120,985 INFO 2019-08-06 13:27:08 MarkDuplicates Written 480,000,000 records. Elapsed time: 01:48:55s. Time for last 10,000,000: 137s. Last read position: chr5:50,502,989 INFO 2019-08-06 13:29:25 MarkDuplicates Written 490,000,000 records. Elapsed time: 01:51:11s. Time for last 10,000,000: 136s. Last read position: chr12:17,978,549 INFO 2019-08-06 13:31:43 MarkDuplicates Written 500,000,000 records. Elapsed time: 01:53:30s. Time for last 10,000,000: 138s. Last read position: chr37:18,829,626 INFO 2019-08-06 13:33:12 MarkDuplicates Before output close freeMemory: 12424962064; totalMemory: 20611858432; maxMemory: 28631367680 INFO 2019-08-06 13:33:13 MarkDuplicates After output close freeMemory: 20764185200; totalMemory: 20811087872; maxMemory: 28631367680 [Tue Aug 06 13:33:13 CDT 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 651.33 minutes. Runtime.totalMemory()=20811087872 [2019-08-06 13:35:55,78] [info] WorkflowManagerActor WorkflowActor-7d60aa8c-c853-4cbb-b320-029db4a1c502 is in a terminal state: WorkflowFailedState [2019-08-06 13:36:27,17] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. [2019-08-06 13:36:30,23] [info] Workflow polling stopped [2019-08-06 13:36:30,28] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds [2019-08-06 13:36:30,28] [info] 0 workflows released by cromid-8c6b3ed [2019-08-06 13:36:30,29] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds [2019-08-06 13:36:30,32] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds [2019-08-06 13:36:30,32] [info] Aborting all running workflows. [2019-08-06 13:36:30,36] [info] JobExecutionTokenDispenser stopped [2019-08-06 13:36:30,43] [info] WorkflowStoreActor stopped [2019-08-06 13:36:30,43] [info] WorkflowLogCopyRouter stopped [2019-08-06 13:36:30,44] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds [2019-08-06 13:36:30,44] [info] WorkflowManagerActor All workflows finished [2019-08-06 13:36:30,44] [info] WorkflowManagerActor stopped [2019-08-06 13:36:31,34] [info] Connection pools shut down [2019-08-06 13:36:31,34] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds [2019-08-06 13:36:31,34] [info] Shutting down JobStoreActor - Timeout = 1800 seconds [2019-08-06 13:36:31,34] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds [2019-08-06 13:36:31,34] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds [2019-08-06 13:36:31,34] [info] Shutting down DockerHashActor - Timeout = 1800 seconds [2019-08-06 13:36:31,34] [info] Shutting down IoProxy - Timeout = 1800 seconds [2019-08-06 13:36:31,34] [info] SubWorkflowStoreActor stopped [2019-08-06 13:36:31,35] [info] KvWriteActor Shutting down: 0 queued messages to process [2019-08-06 13:36:31,35] [info] WriteMetadataActor Shutting down: 0 queued messages to process [2019-08-06 13:36:31,35] [info] CallCacheWriteActor Shutting down: 0 queued messages to process [2019-08-06 13:36:31,35] [info] CallCacheWriteActor stopped [2019-08-06 13:36:31,35] [info] JobStoreActor stopped [2019-08-06 13:36:31,35] [info] IoProxy stopped [2019-08-06 13:36:31,35] [info] DockerHashActor stopped [2019-08-06 13:36:31,35] [info] ServiceRegistryActor stopped [2019-08-06 13:36:31,37] [info] Database closed [2019-08-06 13:36:31,37] [info] Stream materializer shut down [2019-08-06 13:36:31,37] [info] WDL HTTP import resolver closed