| Num | 1 | | ID | task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 | | Name | dedup_bam_1 ctl1 | | Thread | thread_42 | | PID | 5948 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 4 | | Mem | | | | Start | 2016-11-09 17:51:24 | | End | 2016-11-09 18:11:07 | | Elapsed | 00:19:42 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
| | Dependencies | | |
# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
21550 (process ID) old priority 0, new priority 10
|
| Num | 2 | | ID | task.align_bwa.bwa_aln_rep1.line_108.id_10 | | Name | bwa_aln rep1 | | Thread | thread_41 | | PID | 5947 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-11-09 17:51:24 | | End | 2016-11-09 19:11:55 | | Elapsed | 01:20:30 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.sai
| | Dependencies | | |
# SYS command. line 110
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 113
bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.sai
# SYS command. line 115
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
51635 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.17 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.58 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.35 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.97 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.60 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.32 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.54 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.13 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.47 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.16 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19293935 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz
[main] Real time: 4817.132 sec; CPU: 4768.528 sec
|
| Num | 3 | | ID | task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_12 | | Name | markdup_bam_picard ctl1 | | Thread | thread_42 | | PID | 6240 | | | OK | false | | Exit Code | 3 | | Retries | | | State | RUNNING | | Dep. | WAIT | | Cpus | 1 | | Mem | | | | Start | 2016-11-09 18:11:09 | | End | 2016-11-09 18:11:09 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc
| | Dependencies | | |
# SYS command. line 349
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 353
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 354
export MAX_JAVA_MEM="12G"
# SYS command. line 359
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 368
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
46820 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 21:20:15 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Nov 09 21:20:15 PST 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-11-09 21:20:15 MarkDuplicates Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-11-09 21:20:15 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-09 21:20:15 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-11-09 21:20:23 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr1:22,298,551
INFO 2016-11-09 21:20:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:20:30 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 6s. Last read position: chr1:41,895,424
INFO 2016-11-09 21:20:30 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:20:37 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 7s. Last read position: chr1:63,396,527
INFO 2016-11-09 21:20:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:20:45 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 8s. Last read position: chr1:89,147,707
INFO 2016-11-09 21:20:45 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
|
| Num | 4 | | ID | task.align_bwa.bwa_sam_rep1.line_140.id_13 | | Name | bwa_sam rep1 | | Thread | thread_41 | | PID | 6294 | | | OK | false | | Exit Code | 3 | | Retries | | | State | KILLED | | Dep. | ERROR | | Cpus | 1 | | Mem | | | | Start | 2016-11-09 19:11:57 | | End | 2016-11-09 19:31:09 | | Elapsed | 00:19:12 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.sai
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/rep1/SRR1370891_1.flagstat.qc
| | Dependencies | | |
# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 147
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/rep1/SRR1370891_1.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
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