Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/execution/tmp.bPJhLG INFO 23:13:58,711 HelpFormatter - ---------------------------------------------------------------------------------- INFO 23:13:58,717 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 INFO 23:13:58,717 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 23:13:58,717 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 23:13:58,718 HelpFormatter - [Tue Sep 19 23:13:58 EDT 2017] Executing on Linux 3.10.0-327.3.1.el7.x86_64 amd64 INFO 23:13:58,718 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 INFO 23:13:58,724 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/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf -recalFile Yale_SC_All_Chroms_SNPs.recal -tranchesFile Yale_SC_All_Chroms_SNPs.tranches -nt 4 -L /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/WDLScripts/WDLInputFiles/allChroms.intervals -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.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 MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode SNP INFO 23:13:58,728 HelpFormatter - Executing as ag457@compute-a-16-110.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 23:13:58,728 HelpFormatter - Date/Time: 2017/09/19 23:13:58 INFO 23:13:58,728 HelpFormatter - ---------------------------------------------------------------------------------- INFO 23:13:58,729 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 23:13:59,018 GenomeAnalysisEngine - Deflater: IntelDeflater INFO 23:13:59,018 GenomeAnalysisEngine - Inflater: IntelInflater INFO 23:13:59,019 GenomeAnalysisEngine - Strictness is SILENT INFO 23:13:59,156 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 WARN 23:14:00,829 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx because an IOException occurred with message: No locks available. WARN 23:14:00,830 RMDTrackBuilder - Unable to write to /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx for the index file, creating index in memory only WARN 23:14:00,845 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:14:00,846 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:14:08,358 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:14:08,360 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:14:13,749 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:14:13,750 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:16:58,249 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:16:58,251 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 23:21:11,767 IntervalUtils - Processing 3095693981 bp from intervals INFO 23:21:11,783 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 32 processors available on this machine INFO 23:21:11,940 GenomeAnalysisEngine - Preparing for traversal INFO 23:21:11,949 GenomeAnalysisEngine - Done preparing for traversal INFO 23:21:11,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 23:21:11,950 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 23:21:11,950 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 23:21:11,957 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0 INFO 23:21:11,957 TrainingSet - Found omni track: Known = false Training = true Truth = true Prior = Q12.0 INFO 23:21:11,957 TrainingSet - Found 1000G track: Known = false Training = true Truth = false Prior = Q10.0 INFO 23:21:11,958 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0 WARN 23:21:12,023 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:12,029 RMDTrackBuilder - Could not acquire a shared lock on index file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:13,107 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:13,108 RMDTrackBuilder - Could not acquire a shared lock on index file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:14,213 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:14,215 RMDTrackBuilder - Could not acquire a shared lock on index file /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-VariantRecalibratorSNPs/inputs/n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/Yale_SC/bam/test/bam/take6/Variant-Discovery/cromwell-executions/VariantDiscovery/8d8e888d-b775-4170-8b81-20a477eb3b33/call-VariantDiscoveryPerChrom/shard-0/VariantDiscoveryPerChrom/b825e7bb-5331-4c45-9afe-a56929512b49/call-GenotypeGVCFs/execution/Yale_SC_All_Chroms_rawVariants.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:15,256 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:15,257 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:22,337 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:22,338 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:29,619 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:29,620 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/hapmap_3.3.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:37,039 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:37,040 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:41,901 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:41,902 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 23:21:41,955 ProgressMeter - 1:2996522 0.0 30.0 s 49.6 w 0.1% 8.6 h 8.6 h WARN 23:21:46,972 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:46,974 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_omni2.5.b37.vcf.idx, falling back to using an in-memory index for this GATK run. WARN 23:21:52,426 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:21:52,427 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 23:22:11,960 ProgressMeter - 1:2996522 31096.0 60.0 s 32.2 m 0.1% 17.2 h 17.2 h INFO 23:23:11,965 ProgressMeter - 1:2996522 31096.0 120.0 s 64.3 m 0.1% 34.4 h 34.4 h INFO 23:24:11,967 ProgressMeter - 1:2996522 31096.0 3.0 m 96.5 m 0.1% 51.7 h 51.6 h WARN 23:24:27,080 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:24:27,081 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 23:25:11,975 ProgressMeter - 1:2996522 31096.0 4.0 m 2.1 h 0.1% 68.9 h 68.8 h INFO 23:26:11,979 ProgressMeter - 1:2996522 31096.0 5.0 m 2.7 h 0.1% 86.1 h 86.0 h WARN 23:27:01,932 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:27:01,934 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 23:27:11,982 ProgressMeter - 1:4999476 64332.0 6.0 m 93.3 m 0.2% 61.9 h 61.8 h INFO 23:28:11,989 ProgressMeter - 1:4999476 64332.0 7.0 m 108.8 m 0.2% 72.2 h 72.1 h INFO 23:29:11,992 ProgressMeter - 1:4999476 64332.0 8.0 m 2.1 h 0.2% 82.6 h 82.4 h WARN 23:29:36,146 FSLockWithShared$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 23:29:36,147 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 23:30:11,996 ProgressMeter - 1:4999476 64332.0 9.0 m 2.3 h 0.2% 92.9 h 92.7 h INFO 23:31:11,998 ProgressMeter - 1:4999476 64332.0 10.0 m 2.6 h 0.2% 4.3 d 4.3 d INFO 23:32:12,002 ProgressMeter - 1:4999476 64332.0 11.0 m 2.9 h 0.2% 4.7 d 4.7 d INFO 23:33:12,005 ProgressMeter - 1:4999476 64332.0 12.0 m 3.1 h 0.2% 5.2 d 5.2 d WARN 23:33:28,555 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx because an IOException occurred with message: No locks available. INFO 23:33:28,557 RMDTrackBuilder - Could not acquire a shared lock on index file /home/sl279/BiO/Install/GATK-bundle/2.8/b37/dbsnp_138.b37.vcf.idx, falling back to using an in-memory index for this GATK run. INFO 23:34:12,009 ProgressMeter - 1:4999476 64332.0 13.0 m 3.4 h 0.2% 5.6 d 5.6 d INFO 23:35:12,012 ProgressMeter - 1:4999476 64332.0 14.0 m 3.6 h 0.2% 6.0 d 6.0 d INFO 23:36:12,015 ProgressMeter - 1:4999476 64332.0 15.0 m 3.9 h 0.2% 6.5 d 6.4 d INFO 23:37:12,019 ProgressMeter - 1:4999476 64332.0 16.0 m 4.1 h 0.2% 6.9 d 6.9 d WARN 23:37:21,837 FSLockWithShared$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 23:37:21,839 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 23:38:12,022 ProgressMeter - 1:4999476 92815.0 17.0 m 3.1 h 0.2% 7.3 d 7.3 d INFO 23:39:12,025 ProgressMeter - 1:4999476 92815.0 18.0 m 3.2 h 0.2% 7.7 d 7.7 d INFO 23:40:12,036 ProgressMeter - 1:4999476 92815.0 19.0 m 3.4 h 0.2% 8.2 d 8.2 d INFO 23:41:12,039 ProgressMeter - 1:4999476 92815.0 20.0 m 3.6 h 0.2% 8.6 d 8.6 d INFO 23:42:12,043 ProgressMeter - 5:164051951 2.3704888E7 21.0 m 53.0 s 33.8% 62.2 m 41.2 m INFO 23:42:42,045 ProgressMeter - 9:76061782 3.6990989E7 21.5 m 34.0 s 52.2% 41.2 m 19.7 m INFO 23:43:12,049 ProgressMeter - 13:104371262 5.0111178E7 22.0 m 26.0 s 70.7% 31.1 m 9.1 m INFO 23:43:42,052 ProgressMeter - 21:14344393 6.363277E7 22.5 m 21.0 s 90.3% 24.9 m 2.4 m INFO 23:43:53,730 VariantDataManager - QD: mean = 24.57 standard deviation = 5.56 INFO 23:43:53,756 VariantDataManager - MQ: mean = 58.47 standard deviation = 3.98 INFO 23:43:53,779 VariantDataManager - MQRankSum: mean = -0.01 standard deviation = 0.17 INFO 23:43:53,816 VariantDataManager - ReadPosRankSum: mean = 0.05 standard deviation = 0.70 INFO 23:43:53,864 VariantDataManager - FS: mean = 0.06 standard deviation = 0.58 INFO 23:43:53,886 VariantDataManager - SOR: mean = 1.49 standard deviation = 0.78 INFO 23:43:53,906 VariantDataManager - DP: mean = 2.93 standard deviation = 1.43 INFO 23:43:54,071 VariantDataManager - Annotations are now ordered by their information content: [MQ, QD, DP, SOR, MQRankSum, FS, ReadPosRankSum] INFO 23:43:54,086 VariantDataManager - Training with 176690 variants after standard deviation thresholding. INFO 23:43:54,089 GaussianMixtureModel - Initializing model with 100 k-means iterations... INFO 23:44:01,503 VariantRecalibratorEngine - Finished iteration 0. INFO 23:44:05,651 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.62802 INFO 23:44:09,750 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.62767 INFO 23:44:12,054 ProgressMeter - MT:16294 6.8226291E7 23.0 m 20.0 s 100.0% 23.0 m 0.0 s INFO 23:44:14,008 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.08075 INFO 23:44:18,450 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.00507 INFO 23:44:19,346 VariantRecalibratorEngine - Convergence after 21 iterations! INFO 23:44:19,831 VariantRecalibratorEngine - Evaluating full set of 204397 variants... INFO 23:44:42,056 ProgressMeter - MT:16294 6.8226291E7 23.5 m 20.0 s 100.0% 23.5 m 0.0 s INFO 23:44:48,762 VariantDataManager - Selected worst 0 scoring variants --> variants with LOD <= -5.0000. ##### ERROR -- ##### ERROR stack trace org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108) Caused by: java.lang.IllegalArgumentException: No data found. at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:88) at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:536) at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:191) at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226) at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183) ... 5 more ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836): ##### ERROR ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem. ##### ERROR If not, please post the error message, with stack trace, to the GATK forum. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions https://software.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Unable to retrieve result ##### ERROR ------------------------------------------------------------------------------------------