2016/11/06 09:52:24: INFO Starting Job: 15
Cmd is #TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk && \
gatk -T RealignerTargetCreator \
-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/picard/Sample_5_withrg.csorted.cleaned.aligned.bam \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realignment_targets.list
2016/11/06 09:52:29: ERROR INFO 09:52:29,776 HelpFormatter - ——————————————————————————–
INFO 09:52:29,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 09:52:29,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:52:29,808 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
2016/11/06 09:52:29: ERROR INFO 09:52:29,814 HelpFormatter - Program Args: -T RealignerTargetCreator -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/picard/Sample_5_withrg.csorted.cleaned.aligned.bam -o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realignment_targets.list
2016/11/06 09:52:29: ERROR INFO 09:52:29,835 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 09:52:29,835 HelpFormatter - Date/Time: 2016/11/06 09:52:29
INFO 09:52:29,835 HelpFormatter - ——————————————————————————–
INFO 09:52:29,835 HelpFormatter - ——————————————————————————–
2016/11/06 09:52:30: ERROR INFO 09:52:30,188 GenomeAnalysisEngine - Strictness is SILENT
2016/11/06 09:52:30: ERROR INFO 09:52:30,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
2016/11/06 09:52:30: ERROR INFO 09:52:30,984 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
2016/11/06 09:52:31: ERROR INFO 09:52:31,167 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
2016/11/06 09:52:31: ERROR INFO 09:52:31,885 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
2016/11/06 09:52:32: ERROR INFO 09:52:32,156 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:52:32,157 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:52:32,157 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 09:52:32,157 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
2016/11/06 09:53:02: ERROR INFO 09:53:02,211 ProgressMeter - 1:138905645 1.25190144E8 30.0 s 0.0 s 0.3% 2.6 h 2.6 h
2016/11/06 09:53:32: ERROR INFO 09:53:32,233 ProgressMeter - 10:55160893 3.03646214E8 60.0 s 0.0 s 0.7% 2.4 h 2.4 h
2016/11/06 09:54:02: ERROR INFO 09:54:02,265 ProgressMeter - 11:95766281 4.78108724E8 90.0 s 0.0 s 1.1% 2.3 h 2.2 h
2016/11/06 09:54:32: ERROR INFO 09:54:32,298 ProgressMeter - 13:3006601 6.51115775E8 120.0 s 0.0 s 1.5% 2.2 h 2.2 h
2016/11/06 09:55:02: ERROR INFO 09:55:02,309 ProgressMeter - 14:61400613 8.25986215E8 2.5 m 0.0 s 1.9% 2.2 h 2.1 h
2016/11/06 09:55:32: ERROR INFO 09:55:32,338 ProgressMeter - 16:9951653 9.84394562E8 3.0 m 0.0 s 2.3% 2.2 h 2.2 h
2016/11/06 09:56:02: ERROR INFO 09:56:02,357 ProgressMeter - 18:16212357 1.164232652E9 3.5 m 0.0 s 2.7% 2.2 h 2.1 h
2016/11/06 09:56:32: ERROR INFO 09:56:32,398 ProgressMeter - 2:54156637 1.341234433E9 4.0 m 0.0 s 3.1% 2.2 h 2.1 h
2016/11/06 09:57:02: ERROR INFO 09:57:02,427 ProgressMeter - 2:233872033 1.520950529E9 4.5 m 0.0 s 3.5% 2.1 h 2.1 h
2016/11/06 09:58:02: ERROR INFO 09:58:02,489 ProgressMeter - 3:184659289 1.875702532E9 5.5 m 0.0 s 4.3% 2.1 h 2.0 h
2016/11/06 09:58:32: ERROR INFO 09:58:32,579 ProgressMeter - 4:157156113 2.046325515E9 6.0 m 0.0 s 4.7% 2.1 h 2.0 h
2016/11/06 09:59:02: ERROR INFO 09:59:02,622 ProgressMeter - 5:143229553 2.22277751E9 6.5 m 0.0 s 5.1% 2.1 h 2.0 h
2016/11/06 09:59:32: ERROR INFO 09:59:32,647 ProgressMeter - 6:142173349 2.402988665E9 7.0 m 0.0 s 5.5% 2.1 h 119.5 m
2016/11/06 10:00:02: ERROR INFO 10:00:02,681 ProgressMeter - 7:150806293 2.582658388E9 7.5 m 0.0 s 5.9% 2.1 h 118.6 m
2016/11/06 10:00:32: ERROR INFO 10:00:32,708 ProgressMeter - 9:25138857 2.761739861E9 8.0 m 0.0 s 6.4% 2.1 h 117.8 m
2016/11/06 10:01:02: ERROR INFO 10:01:02,732 ProgressMeter - CHR_HG126_PATCH:58462801 2.875001522E9 8.5 m 0.0 s 6.8% 2.1 h 117.3 m
2016/11/06 10:01:32: ERROR INFO 10:01:32,759 ProgressMeter - CHR_HG1342_HG2282_PATCH:34730033 3.086371862E9 9.0 m 0.0 s 7.2% 2.1 h 116.8 m
2016/11/06 10:02:02: ERROR INFO 10:02:02,788 ProgressMeter - CHR_HG1342_HG2282_PATCH:228638133 3.086371862E9 9.5 m 0.0 s 7.6% 2.1 h 115.4 m
2016/11/06 10:02:32: ERROR INFO 10:02:32,799 ProgressMeter - CHR_HG142_HG150_NOVEL_TEST:29172601 3.455501993E9 10.0 m 0.0 s 8.0% 2.1 h 114.6 m
2016/11/06 10:03:02: ERROR INFO 10:03:02,848 ProgressMeter - CHR_HG151_NOVEL_TEST:77810301 3.590596221E9 10.5 m 0.0 s 8.4% 2.1 h 113.8 m
2016/11/06 10:03:33: ERROR INFO 10:03:33,768 ProgressMeter - CHR_HG1651_PATCH:127341501 3.725693917E9 11.0 m 0.0 s 8.9% 2.1 h 113.2 m
2016/11/06 10:04:03: ERROR INFO 10:04:03,807 ProgressMeter - CHR_HG1832_PATCH:138838001 3.896473567E9 11.5 m 0.0 s 9.3% 2.1 h 112.4 m
2016/11/06 10:04:33: ERROR INFO 10:04:33,828 ProgressMeter - CHR_HG2022_PATCH:11183301 4.204066229E9 12.0 m 0.0 s 9.7% 2.1 h 111.8 m
2016/11/06 10:05:03: ERROR INFO 10:05:03,868 ProgressMeter - CHR_HG2022_PATCH:193277493 4.295620021E9 12.5 m 0.0 s 10.1% 2.1 h 111.1 m
2016/11/06 10:05:33: ERROR INFO 10:05:33,890 ProgressMeter - CHR_HG2058_PATCH:35424265 4.567315499E9 13.0 m 0.0 s 10.5% 2.1 h 110.5 m
2016/11/06 10:06:03: ERROR INFO 10:06:03,923 ProgressMeter - CHR_HG2058_PATCH:214737465 4.567315499E9 13.5 m 0.0 s 11.0% 2.1 h 109.9 m
2016/11/06 10:06:33: ERROR INFO 10:06:33,945 ProgressMeter - CHR_HG2066_PATCH:87536201 4.846975629E9 14.0 m 0.0 s 11.4% 2.1 h 109.3 m
2016/11/06 10:07:03: ERROR INFO 10:07:03,979 ProgressMeter - CHR_HG2095_PATCH:76320861 5.062720144E9 14.5 m 0.0 s 11.8% 2.1 h 108.6 m
2016/11/06 10:07:33: ERROR INFO 10:07:33,991 ProgressMeter - CHR_HG2104_PATCH:15901401 5.294230315E9 15.0 m 0.0 s 12.2% 2.0 h 107.8 m
2016/11/06 10:08:04: ERROR INFO 10:08:04,029 ProgressMeter - CHR_HG2104_PATCH:201611849 5.407230763E9 15.5 m 0.0 s 12.7% 2.0 h 107.1 m
2016/11/06 10:08:34: ERROR INFO 10:08:34,051 ProgressMeter - CHR_HG2128_PATCH:138344401 5.543188574E9 16.0 m 0.0 s 13.1% 2.0 h 106.4 m
2016/11/06 10:09:04: ERROR INFO 10:09:04,079 ProgressMeter - CHR_HG2216_PATCH:17565501 5.847799737E9 16.5 m 0.0 s 13.5% 2.0 h 105.8 m
2016/11/06 10:09:34: ERROR INFO 10:09:34,119 ProgressMeter - CHR_HG2217_PATCH:88115101 5.962176165E9 17.0 m 0.0 s 13.9% 2.0 h 105.1 m
2016/11/06 10:10:04: ERROR INFO 10:10:04,139 ProgressMeter - CHR_HG2232_PATCH:130669801 6.097262786E9 17.5 m 0.0 s 14.3% 2.0 h 104.6 m
2016/11/06 10:10:34: ERROR INFO 10:10:34,159 ProgressMeter - CHR_HG2233_PATCH:67358201 6.339456315E9 18.0 m 0.0 s 14.8% 2.0 h 104.2 m
2016/11/06 10:11:04: ERROR INFO 10:11:04,198 ProgressMeter - CHR_HG2235_PATCH:11430201 6.58164985E9 18.5 m 0.0 s 15.2% 2.0 h 103.5 m
2016/11/06 10:11:34: ERROR INFO 10:11:34,220 ProgressMeter - CHR_HG2235_PATCH:198295645 6.647857594E9 19.0 m 0.0 s 15.6% 2.0 h 102.9 m
2016/11/06 10:12:04: ERROR INFO 10:12:04,247 ProgressMeter - CHR_HG2237_PATCH:185071269 6.870499873E9 19.5 m 0.0 s 16.0% 2.0 h 102.3 m
2016/11/06 10:12:34: ERROR INFO 10:12:34,278 ProgressMeter - CHR_HG2241_PATCH:8496601 7.137581153E9 20.0 m 0.0 s 16.5% 2.0 h 101.7 m
2016/11/06 10:13:04: ERROR INFO 10:13:04,304 ProgressMeter - CHR_HG2242_HG2243_PATCH:56133701 7.271373875E9 20.5 m 0.0 s 16.9% 2.0 h 101.2 m
2016/11/06 10:13:34: ERROR INFO 10:13:34,317 ProgressMeter - CHR_HG2244_HG2245_PATCH:101366601 7.444492772E9 21.0 m 0.0 s 17.3% 2.0 h 100.6 m
2016/11/06 10:14:04: ERROR INFO 10:14:04,330 ProgressMeter - CHR_HG2249_PATCH:10334201 7.672242597E9 21.5 m 0.0 s 17.7% 2.0 h 100.2 m