Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/execution/tmp.5q02mc INFO 20:05:08,333 HelpFormatter - ---------------------------------------------------------------------------------- INFO 20:05:08,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 INFO 20:05:08,335 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 20:05:08,335 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 20:05:08,336 HelpFormatter - [Sun Sep 10 20:05:08 EDT 2017] Executing on Linux 3.10.0-327.3.1.el7.x86_64 amd64 INFO 20:05:08,336 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 INFO 20:05:08,339 HelpFormatter - Program Args: -T VariantRecalibrator -R /home/sl279/BiO/Install/GATK-bundle/2.8/b37/human_g1k_v37_decoy.fasta -input /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf -recalFile Synapse_MT_Indels.recal -tranchesFile Synapse_MT_Indels.tranches -nt 4 --maxGaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12.0 /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf -an QD -an DP -an FS -an SOR -an ReadPosRankSum -an MQRankSum -mode INDEL INFO 20:05:08,342 HelpFormatter - Executing as ag457@compute-a-16-94.o2.rc.hms.harvard.edu on Linux 3.10.0-327.3.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14. INFO 20:05:08,342 HelpFormatter - Date/Time: 2017/09/10 20:05:08 INFO 20:05:08,343 HelpFormatter - ---------------------------------------------------------------------------------- INFO 20:05:08,343 HelpFormatter - ---------------------------------------------------------------------------------- ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/n/data1/hms/dbmi/park/alon/0_GATK_Tools/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console... INFO 20:05:08,715 GenomeAnalysisEngine - Deflater: IntelDeflater INFO 20:05:08,716 GenomeAnalysisEngine - Inflater: IntelInflater INFO 20:05:08,717 GenomeAnalysisEngine - Strictness is SILENT INFO 20:05:08,847 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 WARN 20:05:08,956 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx because an IOException occurred with message: No locks available. WARN 20:05:08,958 RMDTrackBuilder - Unable to write to /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx for the index file, creating index in memory only WARN 20:05:08,975 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:05:08,975 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 20:05:13,638 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:05:13,639 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 20:09:29,878 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 32 processors available on this machine INFO 20:09:29,943 GenomeAnalysisEngine - Preparing for traversal INFO 20:09:29,949 GenomeAnalysisEngine - Done preparing for traversal INFO 20:09:29,950 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 20:09:29,950 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 20:09:29,950 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 20:09:29,963 TrainingSet - Found mills track: Known = false Training = true Truth = true Prior = Q12.0 INFO 20:09:29,963 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0 WARN 20:09:30,051 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx because an IOException occurred with message: No locks available. INFO 20:09:30,053 RMDTrackBuilder - Could not acquire a shared lock on index file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 20:09:30,076 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx because an IOException occurred with message: No locks available. INFO 20:09:30,089 RMDTrackBuilder - Could not acquire a shared lock on index file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 20:09:30,117 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx because an IOException occurred with message: No locks available. INFO 20:09:30,120 RMDTrackBuilder - Could not acquire a shared lock on index file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-VariantRecalibratorIndels/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take5/Variant-Discovery/cromwell-executions/VariantDiscovery/dfde0df3-b8c6-4c0f-8238-07bd3b86826b/call-VariantDiscoveryPerChrom/shard-24/VariantDiscoveryPerChrom/70c2716a-6bcb-4a04-b1ca-4a5de4bcd398/call-GenotypeGVCFs/execution/Synapse_MT_rawVariants.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 20:09:30,144 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:09:30,146 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 20:09:33,438 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:09:33,449 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 20:09:36,579 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:09:36,581 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 20:09:39,649 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:09:39,652 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 20:09:59,956 ProgressMeter - 1:3996712 0.0 30.0 s 49.6 w 0.1% 6.5 h 6.5 h INFO 20:10:29,960 ProgressMeter - 1:3996712 0.0 60.0 s 99.2 w 0.1% 13.1 h 13.1 h INFO 20:11:30,008 ProgressMeter - 1:3996712 0.0 120.0 s 198.5 w 0.1% 26.2 h 26.1 h INFO 20:12:30,011 ProgressMeter - 1:3996712 0.0 3.0 m 297.7 w 0.1% 39.3 h 39.2 h INFO 20:13:30,014 ProgressMeter - 1:3996712 0.0 4.0 m 396.9 w 0.1% 52.3 h 52.3 h WARN 20:14:26,807 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:14:26,808 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 20:14:30,023 ProgressMeter - 1:3996712 0.0 5.0 m 496.2 w 0.1% 65.4 h 65.3 h INFO 20:15:30,025 ProgressMeter - 1:3996712 0.0 6.0 m 595.4 w 0.1% 78.5 h 78.4 h INFO 20:16:30,035 ProgressMeter - 1:3996712 0.0 7.0 m 694.6 w 0.1% 91.6 h 91.5 h INFO 20:17:30,044 ProgressMeter - 1:3996712 0.0 8.0 m 793.8 w 0.1% 4.4 d 4.4 d INFO 20:18:30,049 ProgressMeter - 1:3996712 0.0 9.0 m 893.0 w 0.1% 4.9 d 4.9 d WARN 20:19:19,827 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 20:19:19,829 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 20:19:30,062 ProgressMeter - 1:3996712 0.0 10.0 m 992.2 w 0.1% 5.5 d 5.4 d INFO 20:20:30,065 ProgressMeter - 1:3996712 0.0 11.0 m 1091.5 w 0.1% 6.0 d 6.0 d INFO 20:21:30,068 ProgressMeter - 1:3996712 0.0 12.0 m 1190.7 w 0.1% 6.5 d 6.5 d INFO 20:22:30,072 ProgressMeter - 1:3996712 0.0 13.0 m 1289.9 w 0.1% 7.1 d 7.1 d INFO 20:23:30,074 ProgressMeter - 1:3996712 0.0 14.0 m 1389.1 w 0.1% 7.6 d 7.6 d INFO 20:24:30,076 ProgressMeter - 3:60286856 1.2325334E7 15.0 m 73.0 s 17.6% 85.1 m 70.1 m INFO 20:25:00,078 ProgressMeter - 7:70081821 3.0145856E7 15.5 m 30.0 s 41.6% 37.3 m 21.8 m INFO 20:25:30,080 ProgressMeter - 12:41991095 4.6109981E7 16.0 m 20.0 s 63.5% 25.2 m 9.2 m INFO 20:26:00,081 ProgressMeter - 19:57131239 6.2172731E7 16.5 m 15.0 s 86.6% 19.1 m 2.6 m ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836): ##### ERROR ##### ERROR This means that one or more arguments or inputs in your command are incorrect. ##### ERROR The error message below tells you what is the problem. ##### ERROR ##### ERROR If the problem is an invalid argument, please check the online documentation guide ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ##### ERROR ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions https://software.broadinstitute.org/gatk ##### ERROR ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ##### ERROR ##### ERROR MESSAGE: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. ##### ERROR ------------------------------------------------------------------------------------------