2016/11/06 09:51:57: INFO Starting Job: 9
Cmd is #TASK tags=Sample_5
picard -Xmx2g CollectMultipleMetrics \
TMP_DIR=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp \
I=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_csorted.cleaned.aligned.bam \
O=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned \
PROGRAM=CollectAlignmentSummaryMetrics PROGRAM=CollectInsertSizeMetrics PROGRAM=QualityScoreDistribution PROGRAM=MeanQualityByCycle
2016/11/06 09:51:58: ERROR [Sun Nov 06 09:51:58 GST 2016] picard.analysis.CollectMultipleMetrics INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_csorted.cleaned.aligned.bam OUTPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] TMP_DIR=[/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp] ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
2016/11/06 09:51:58: ERROR [Sun Nov 06 09:51:58 GST 2016] 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; Picard version: 2.5.0(2c370988aefe41f579920c8a6a678a201c5261c1_1466708365)
2016/11/06 09:52:02: ERROR INFO 2016-11-06 09:52:02 RExecutor Executing R script via command: Rscript /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp/script5169277710540645794.R /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.base_distribution_by_cycle_metrics /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.base_distribution_by_cycle.pdf Sample_5_csorted.cleaned.aligned.bam
2016/11/06 09:52:05: ERROR INFO 2016-11-06 09:52:05 ProcessExecutor null device
INFO 2016-11-06 09:52:05 ProcessExecutor 1
2016/11/06 09:52:12: ERROR INFO 2016-11-06 09:52:12 RExecutor Executing R script via command: Rscript /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp/script7011113815525516007.R /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.insert_size_metrics /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.insert_size_histogram.pdf Sample_5_csorted.cleaned.aligned.bam
2016/11/06 09:52:14: ERROR INFO 2016-11-06 09:52:14 ProcessExecutor null device
INFO 2016-11-06 09:52:14 ProcessExecutor 1
2016/11/06 09:52:14: ERROR INFO 2016-11-06 09:52:14 RExecutor Executing R script via command: Rscript /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp/script4094347614302844414.R /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.quality_by_cycle_metrics /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.quality_by_cycle.pdf Sample_5_csorted.cleaned.aligned.bam
2016/11/06 09:52:15: ERROR INFO 2016-11-06 09:52:15 ProcessExecutor null device
INFO 2016-11-06 09:52:15 ProcessExecutor 1
2016/11/06 09:52:15: ERROR INFO 2016-11-06 09:52:15 RExecutor Executing R script via command: Rscript /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp/script2018843830008339836.R /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.quality_distribution_metrics /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_collmulmetr.csorted.cleaned.aligned.quality_distribution.pdf Sample_5_csorted.cleaned.aligned.bam
2016/11/06 09:52:16: ERROR INFO 2016-11-06 09:52:16 ProcessExecutor null device
INFO 2016-11-06 09:52:16 ProcessExecutor 1
2016/11/06 09:52:16: ERROR [Sun Nov 06 09:52:16 GST 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.31 minutes.
Runtime.totalMemory()=1446510592
2016/11/06 09:52:16: INFO Finishing job 9 with ExitCode 0
2016/11/06 09:52:16: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 19 seconds