2016/11/06 11:53:54: INFO Starting Job: 19
Cmd is #TASK tags=Sample_5
gatk -T HaplotypeCaller \
-R /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa \
-I /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realigned.withrg.csorted.cleaned.aligned.bam \
-stand_emit_conf 10 -stand_call_conf 30 –genotyping_mode DISCOVERY \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf
2016/11/06 11:53:58: ERROR INFO 11:53:58,425 HelpFormatter - ——————————————————————————–
INFO 11:53:58,428 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 11:53:58,429 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:53:58,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:53:58,432 HelpFormatter - Program Args: -T HaplotypeCaller -R /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa -I /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realigned.withrg.csorted.cleaned.aligned.bam -stand_emit_conf 10 -stand_call_conf 30 –genotyping_mode DISCOVERY -o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf
2016/11/06 11:53:58: ERROR INFO 11:53:58,456 HelpFormatter - Executing as gencore@compute-21-1.local on Linux 3.10.0-327.10.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15.
INFO 11:53:58,456 HelpFormatter - Date/Time: 2016/11/06 11:53:58
INFO 11:53:58,456 HelpFormatter - ——————————————————————————–
INFO 11:53:58,456 HelpFormatter - ——————————————————————————–
2016/11/06 11:53:58: ERROR INFO 11:53:58,625 GenomeAnalysisEngine - Strictness is SILENT
2016/11/06 11:53:58: ERROR INFO 11:53:58,987 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
2016/11/06 11:53:59: ERROR INFO 11:53:59,016 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
2016/11/06 11:53:59: ERROR INFO 11:53:59,186 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
2016/11/06 11:53:59: ERROR INFO 11:53:59,317 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
2016/11/06 11:53:59: ERROR INFO 11:53:59,438 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
2016/11/06 11:53:59: ERROR INFO 11:53:59,626 GenomeAnalysisEngine - Done preparing for traversal
2016/11/06 11:53:59: ERROR INFO 11:53:59,639 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
2016/11/06 11:53:59: ERROR INFO 11:53:59,640 ProgressMeter - | processed | time | per 1M | | total | remaining
2016/11/06 11:53:59: ERROR INFO 11:53:59,641 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
2016/11/06 11:53:59: ERROR INFO 11:53:59,679 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output
2016/11/06 11:53:59: ERROR INFO 11:53:59,772 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
WARN 11:53:59,772 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
INFO 11:53:59,772 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
2016/11/06 11:54:00: ERROR INFO 11:53:59,986 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
2016/11/06 11:54:06: ERROR Using SSE4.1 accelerated implementation of PairHMM
2016/11/06 11:54:07: ERROR INFO 11:54:06,980 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
INFO 11:54:06,980 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
2016/11/06 11:54:29: ERROR INFO 11:54:29,826 ProgressMeter - 1:49421386 0.0 30.0 s 49.9 w 0.1% 7.3 h 7.3 h
2016/11/06 11:54:59: ERROR INFO 11:54:59,842 ProgressMeter - 1:149858468 0.0 60.0 s 99.5 w 0.3% 4.8 h 4.8 h
2016/11/06 11:55:29: ERROR INFO 11:55:29,867 ProgressMeter - 1:247929576 0.0 90.0 s 149.2 w 0.6% 4.4 h 4.4 h
2016/11/06 11:55:59: ERROR INFO 11:55:59,897 ProgressMeter - 10:73486808 2.48956422E8 120.0 s 0.0 s 0.7% 4.5 h 4.5 h
2016/11/06 11:56:29: ERROR INFO 11:56:29,916 ProgressMeter - 11:22453425 3.82753844E8 2.5 m 0.0 s 0.9% 4.5 h 4.4 h
2016/11/06 11:56:59: ERROR INFO 11:56:59,959 ProgressMeter - 11:116221250 3.82753844E8 3.0 m 0.0 s 1.1% 4.4 h 4.3 h
2016/11/06 11:57:29: ERROR INFO 11:57:29,997 ProgressMeter - 12:95685715 5.17840466E8 3.5 m 0.0 s 1.4% 4.1 h 4.1 h
2016/11/06 11:58:00: ERROR INFO 11:58:00,047 ProgressMeter - 13:48380502 6.51115775E8 4.0 m 0.0 s 1.6% 4.1 h 4.1 h
2016/11/06 11:58:30: ERROR INFO 11:58:30,128 ProgressMeter - 14:33338476 7.65480103E8 4.5 m 0.0 s 1.8% 4.1 h 4.0 h
2016/11/06 11:59:00: ERROR INFO 11:59:00,177 ProgressMeter - 15:30370971 8.72523821E8 5.0 m 0.0 s 2.1% 4.0 h 3.9 h
2016/11/06 11:59:30: ERROR INFO 11:59:30,208 ProgressMeter - 16:25932239 9.7451501E8 5.5 m 0.0 s 2.3% 4.0 h 3.9 h
2016/11/06 12:00:00: ERROR INFO 12:00:00,227 ProgressMeter - 17:31468144 1.064853355E9 6.0 m 0.0 s 2.5% 4.0 h 3.9 h
2016/11/06 12:00:30: ERROR INFO 12:00:30,230 ProgressMeter - 18:43964554 1.148110796E9 6.5 m 0.0 s 2.7% 3.9 h 3.8 h
2016/11/06 12:01:00: ERROR INFO 12:01:00,249 ProgressMeter - 2:8038968 1.287101697E9 7.0 m 0.0 s 3.0% 3.9 h 3.8 h
2016/11/06 12:01:30: ERROR INFO 12:01:30,288 ProgressMeter - 2:107035309 1.287101697E9 7.5 m 0.0 s 3.2% 3.9 h 3.8 h
2016/11/06 12:02:00: ERROR INFO 12:02:00,308 ProgressMeter - 2:218345576 1.287101697E9 8.0 m 0.0 s 3.5% 3.8 h 3.7 h
2016/11/06 12:02:30: ERROR INFO 12:02:30,329 ProgressMeter - 21:21920178 1.593739393E9 8.5 m 0.0 s 3.7% 3.8 h 3.7 h
2016/11/06 12:03:00: ERROR INFO 12:03:00,359 ProgressMeter - 3:24573103 1.691267844E9 9.0 m 0.0 s 4.0% 3.8 h 3.6 h
2016/11/06 12:03:30: ERROR INFO 12:03:30,397 ProgressMeter - 3:125003864 1.691267844E9 9.5 m 0.0 s 4.2% 3.8 h 3.6 h
2016/11/06 12:04:00: ERROR INFO 12:04:00,928 ProgressMeter - 4:40181013 1.889563403E9 10.0 m 0.0 s 4.4% 3.8 h 3.6 h
2016/11/06 12:04:30: ERROR INFO 12:04:30,949 ProgressMeter - 4:159037912 1.889563403E9 10.5 m 0.0 s 4.7% 3.7 h 3.5 h
2016/11/06 12:05:00: ERROR INFO 12:05:00,969 ProgressMeter - 5:82359381 2.079777958E9 11.0 m 0.0 s 5.0% 3.7 h 3.5 h
2016/11/06 12:05:31: ERROR INFO 12:05:31,009 ProgressMeter - 6:5179008 2.261316217E9 11.5 m 0.0 s 5.2% 3.7 h 3.5 h
2016/11/06 12:06:01: ERROR INFO 12:06:01,048 ProgressMeter - 6:116718887 2.261316217E9 12.0 m 0.0 s 5.5% 3.7 h 3.5 h
2016/11/06 12:06:31: ERROR INFO 12:06:31,069 ProgressMeter - 7:52809598 2.432122196E9 12.5 m 0.0 s 5.7% 3.6 h 3.4 h
2016/11/06 12:07:01: ERROR INFO 12:07:01,444 ProgressMeter - 8:140404 2.591468169E9 13.0 m 0.0 s 6.0% 3.6 h 3.4 h
2016/11/06 12:07:31: ERROR INFO 12:07:31,487 ProgressMeter - 8:113803897 2.591468169E9 13.5 m 0.0 s 6.2% 3.6 h 3.4 h
2016/11/06 12:08:01: ERROR INFO 12:08:01,502 ProgressMeter - 9:67993298 2.736606805E9 14.0 m 0.0 s 6.5% 3.6 h 3.4 h
2016/11/06 12:08:31: ERROR INFO 12:08:31,528 ProgressMeter - CHR_HG126_PATCH:38297800 2.875001522E9 14.5 m 0.0 s 6.7% 3.6 h 3.4 h
2016/11/06 12:09:01: ERROR INFO 12:09:01,548 ProgressMeter - CHR_HG126_PATCH:162773800 2.875001522E9 15.0 m 0.0 s 7.0% 3.6 h 3.3 h
2016/11/06 12:09:31: ERROR INFO 12:09:31,562 ProgressMeter - CHR_HG1342_HG2282_PATCH:81293917 3.07329743E9 15.5 m 0.0 s 7.3% 3.6 h 3.3 h
2016/11/06 12:10:01: ERROR INFO 12:10:01,588 ProgressMeter - CHR_HG1342_HG2282_PATCH:199917307 3.07329743E9 16.0 m 0.0 s 7.5% 3.5 h 3.3 h
2016/11/06 12:10:31: ERROR INFO 12:10:31,607 ProgressMeter - CHR_HG1362_PATCH:68243548 3.322226679E9 16.5 m 0.0 s 7.8% 3.5 h 3.3 h
2016/11/06 12:11:01: ERROR INFO 12:11:01,609 ProgressMeter - CHR_HG142_HG150_NOVEL_TEST:58403500 3.455501993E9 17.0 m 0.0 s 8.1% 3.5 h 3.2 h