2016/11/06 09:52:14: INFO Starting Job: 10
Cmd is #TASK tags=Sample_5
picard -Xmx2g MarkDuplicates \
M=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_markDup_metrics_file.txt \
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/picard/Sample_5_mdup.withrg.csorted.cleaned.aligned.bam \
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=100 \
TMP_DIR=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp
2016/11/06 09:52:15: ERROR [Sun Nov 06 09:52:15 GST 2016] picard.sam.markduplicates.MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=100 INPUT=[/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_withrg.csorted.cleaned.aligned.bam] OUTPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_mdup.withrg.csorted.cleaned.aligned.bam METRICS_FILE=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_markDup_metrics_file.txt TMP_DIR=[/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=
2016/11/06 09:52:15: ERROR [Sun Nov 06 09:52:15 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 09:52:15: ERROR INFO 2016-11-06 09:52:15 MarkDuplicates Start of doWork freeMemory: 1509865608; totalMemory: 1519386624; maxMemory: 1908932608
INFO 2016-11-06 09:52:15 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-06 09:52:15 MarkDuplicates Will retain up to 7342048 data points before spilling to disk.
2016/11/06 09:52:21: ERROR INFO 2016-11-06 09:52:21 MarkDuplicates Read 239438 records. 0 pairs never matched.
2016/11/06 09:52:22: ERROR INFO 2016-11-06 09:52:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1425083440; totalMemory: 1519386624; maxMemory: 1908932608
INFO 2016-11-06 09:52:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
2016/11/06 09:52:22: ERROR INFO 2016-11-06 09:52:22 MarkDuplicates Traversing read pair information and detecting duplicates.
2016/11/06 09:52:22: ERROR INFO 2016-11-06 09:52:22 MarkDuplicates Traversing fragment information and detecting duplicates.
2016/11/06 09:52:23: ERROR INFO 2016-11-06 09:52:23 MarkDuplicates Sorting list of duplicate records.
2016/11/06 09:52:23: ERROR
2016/11/06 09:52:23: ERROR INFO 2016-11-06 09:52:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 1215927760; totalMemory: 1706557440; maxMemory: 1908932608
2016/11/06 09:52:23: ERROR INFO 2016-11-06 09:52:23 MarkDuplicates Marking 59141 records as duplicates.
INFO 2016-11-06 09:52:23 MarkDuplicates Found 10 optical duplicate clusters.
2016/11/06 09:52:23: ERROR INFO 2016-11-06 09:52:23 MarkDuplicates Reads are assumed to be ordered by: coordinate
2016/11/06 09:52:23: ERROR
2016/11/06 09:52:30: ERROR INFO 2016-11-06 09:52:30 MarkDuplicates Before output close freeMemory: 1692313096; totalMemory: 1706557440; maxMemory: 1908932608
2016/11/06 09:52:30: ERROR INFO 2016-11-06 09:52:30 MarkDuplicates After output close freeMemory: 1692378192; totalMemory: 1706557440; maxMemory: 1908932608
2016/11/06 09:52:30: ERROR [Sun Nov 06 09:52:30 GST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.25 minutes.
Runtime.totalMemory()=1706557440
2016/11/06 09:52:30: INFO Finishing job 10 with ExitCode -1
2016/11/06 09:52:30: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 16 seconds