2016/11/06 11:52:12: INFO Starting Job: 16
Cmd is #TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk && \
gatk -T IndelRealigner \
-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 \
-targetIntervals /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realignment_targets.list \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realigned.withrg.csorted.cleaned.aligned.bam
2016/11/06 11:52:17: ERROR INFO 11:52:17,389 HelpFormatter - ——————————————————————————–
INFO 11:52:17,391 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 11:52:17,391 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:52:17,391 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:52:17,394 HelpFormatter - Program Args: -T IndelRealigner -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 -targetIntervals /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realignment_targets.list -o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realigned.withrg.csorted.cleaned.aligned.bam
2016/11/06 11:52:17: ERROR INFO 11:52:17,488 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 11:52:17,488 HelpFormatter - Date/Time: 2016/11/06 11:52:17
INFO 11:52:17,489 HelpFormatter - ——————————————————————————–
INFO 11:52:17,489 HelpFormatter - ——————————————————————————–
2016/11/06 11:52:17: ERROR INFO 11:52:17,946 GenomeAnalysisEngine - Strictness is SILENT
2016/11/06 11:52:18: ERROR INFO 11:52:18,523 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:52:18,529 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
2016/11/06 11:52:18: ERROR INFO 11:52:18,735 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.18
2016/11/06 11:52:19: ERROR INFO 11:52:19,452 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 11:52:19,455 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:52:19,456 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:52:19,456 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:52:19,456 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
2016/11/06 11:52:19: ERROR INFO 11:52:19,577 ReadShardBalancer$1 - Loading BAM index data
INFO 11:52:19,578 ReadShardBalancer$1 - Done loading BAM index data
2016/11/06 11:52:49: ERROR INFO 11:52:49,503 ProgressMeter - 2:29275212 130260.0 30.0 s 3.8 m 3.0% 16.5 m 16.0 m
2016/11/06 11:53:15: ERROR INFO 11:53:15,879 ProgressMeter - done 240156.0 56.0 s 3.9 m 100.0% 56.0 s 0.0 s
INFO 11:53:15,880 ProgressMeter - Total runtime 56.42 secs, 0.94 min, 0.02 hours
2016/11/06 11:53:15: ERROR INFO 11:53:15,885 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 240156 total reads (0.00%)
INFO 11:53:15,885 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 11:53:15,885 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
2016/11/06 11:53:46: INFO Finishing job 16 with ExitCode 0
2016/11/06 11:53:46: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 01 minutes, 34 seconds