2016/11/06 09:51:18: INFO Starting Job: 3
Cmd is #TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard && \
picard -Xmx2g CleanSam \
INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam \
O=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_cleaned.aligned.bam \
TMP_DIR=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp
2016/11/06 09:51:30: ERROR [Sun Nov 06 09:51:30 GST 2016] picard.sam.CleanSam INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam OUTPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_cleaned.aligned.bam TMP_DIR=[/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp] 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 09:51:30: ERROR [Sun Nov 06 09:51:30 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 09:51:38: ERROR [Sun Nov 06 09:51:38 GST 2016] picard.sam.CleanSam done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1519386624
2016/11/06 09:51:38: INFO Finishing job 3 with ExitCode 0
2016/11/06 09:51:38: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 20 seconds