2016/11/06 09:51:43: INFO Starting Job: 4
Cmd is #TASK tags=Sample_5
picard -Xmx2g SortSam \
INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_cleaned.aligned.bam \
O=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_csorted.cleaned.aligned.bam \
SO=coordinate \
TMP_DIR=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp
2016/11/06 09:51:44: ERROR [Sun Nov 06 09:51:44 GST 2016] picard.sam.SortSam INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_cleaned.aligned.bam OUTPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_csorted.cleaned.aligned.bam SORT_ORDER=coordinate 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 09:51:44: ERROR [Sun Nov 06 09:51:44 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 09:51:48: ERROR INFO 2016-11-06 09:51:48 SortSam Finished reading inputs, merging and writing to output now.
2016/11/06 09:51:52: ERROR [Sun Nov 06 09:51:52 GST 2016] picard.sam.SortSam done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1519386624
2016/11/06 09:51:52: INFO Finishing job 4 with ExitCode -1
2016/11/06 09:51:52: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 09 seconds