| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161110_171037_465 |
| Start time | 2016-11-10 17:10:37 |
| Run time | 2 days 19:56:23.922 |
| Tasks executed | 5 |
| Tasks failed | 2 |
| Tasks failed names | markdup_bam_picard ctl1 dedup_bam_1 rep1 |
| Arguments* | [-title, SRR1370902_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370902_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_42 | thread_Root | chipseq.bds.20161110_171037_465_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161110_171037_465_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 |
| thread_41 | thread_Root | chipseq.bds.20161110_171037_465_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11 chipseq.bds.20161110_171037_465_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 chipseq.bds.20161110_171037_465_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_14 |
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_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/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_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/SRR1370902_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-------------------- 12259 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 110
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/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/SRR1370902_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_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-------------------- 12274 (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] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.94 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.70 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.83 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.65 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.63 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.68 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.35 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.42 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.29 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.08 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.95 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.06 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.8% 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] 11010048 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.52 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.40 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.23 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.42 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.71 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.05 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.00 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.38 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.06 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.88 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.03 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.06 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.24 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.36 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.68 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.28 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.24 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.01 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 12.07 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 23662830 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/SRR1370902_1.fastq.gz [main] Real time: 3825.784 sec; CPU: 3813.628 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 354
export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"
# SYS command. line 360
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 369
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_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/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 19643 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Nov 10 20:00:40 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_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 [Thu Nov 10 20:00:40 PST 2016] Executing as imk1@wotan on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-10 20:00:41 MarkDuplicates Start of doWork freeMemory: 254877736; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-10 20:00:41 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-10 20:00:41 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-10 20:01:07 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 22s. Last read position: chr1:22,298,551 INFO 2016-11-10 20:01:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:01:18 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 10s. Last read position: chr1:41,895,424 INFO 2016-11-10 20:01:18 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:01:33 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 14s. Last read position: chr1:63,396,527 INFO 2016-11-10 20:01:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:02:02 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 29s. Last read position: chr1:89,147,707 INFO 2016-11-10 20:02:02 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:02:30 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 27s. Last read position: chr1:115,615,553 INFO 2016-11-10 20:02:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:02:51 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 20s. Last read position: chr1:164,468,682 INFO 2016-11-10 20:02:51 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:03:23 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 32s. Last read position: chr1:189,102,252 INFO 2016-11-10 20:03:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:03:52 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 29s. Last read position: chr1:213,979,760 INFO 2016-11-10 20:03:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:04:29 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 36s. Last read position: chr1:231,814,268 INFO 2016-11-10 20:04:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:05:25 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 56s. Last read position: chr2:3,652,468 INFO 2016-11-10 20:05:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:06:08 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 42s. Last read position: chr2:39,505,122 INFO 2016-11-10 20:06:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:06:47 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 38s. Last read position: chr2:73,561,393 INFO 2016-11-10 20:06:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:07:33 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 46s. Last read position: chr2:120,526,571 INFO 2016-11-10 20:07:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:08:21 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 48s. Last read position: chr2:160,316,783 INFO 2016-11-10 20:08:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:09:18 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 56s. Last read position: chr2:195,549,735 INFO 2016-11-10 20:09:18 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:10:43 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 85s. Last read position: chr2:230,358,034 INFO 2016-11-10 20:10:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:12:03 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 79s. Last read position: chr3:16,305,780 INFO 2016-11-10 20:12:03 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:13:17 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 74s. Last read position: chr3:49,251,279 INFO 2016-11-10 20:13:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:14:32 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 74s. Last read position: chr3:84,621,225 INFO 2016-11-10 20:14:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:15:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 36s. Last read position: chr3:128,121,129 INFO 2016-11-10 20:15:09 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:16:45 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 96s. Last read position: chr3:165,373,238 INFO 2016-11-10 20:16:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:17:22 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:16:38s. Time for last 1,000,000: 37s. Last read position: chr3:195,333,247 INFO 2016-11-10 20:17:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:18:25 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:17:41s. Time for last 1,000,000: 63s. Last read position: chr4:37,752,582 INFO 2016-11-10 20:18:25 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:19:56 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:19:12s. Time for last 1,000,000: 90s. Last read position: chr4:81,286,306 INFO 2016-11-10 20:19:56 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:20:54 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:20:09s. Time for last 1,000,000: 57s. Last read position: chr4:119,339,736 INFO 2016-11-10 20:20:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:21:22 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:20:37s. Time for last 1,000,000: 27s. Last read position: chr4:158,818,783 INFO 2016-11-10 20:21:22 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:23:14 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:22:30s. Time for last 1,000,000: 112s. Last read position: chr5:6,447,551 INFO 2016-11-10 20:23:14 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-11-10 20:24:25 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:23:41s. Time for last 1,000,000: 71s. Last read position: chr5:33,219,021 INFO 2016-11-10 20:24:25 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:26:37 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:25:52s. Time for last 1,000,000: 131s. Last read position: chr5:60,694,078 INFO 2016-11-10 20:26:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:27:38 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:26:54s. Time for last 1,000,000: 61s. Last read position: chr5:86,336,676 INFO 2016-11-10 20:27:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:31:35 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:30:50s. Time for last 1,000,000: 236s. Last read position: chr5:112,930,184 INFO 2016-11-10 20:31:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:33:07 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:32:23s. Time for last 1,000,000: 92s. Last read position: chr5:136,852,889 INFO 2016-11-10 20:33:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:36:49 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:36:04s. Time for last 1,000,000: 221s. Last read position: chr5:160,271,193 INFO 2016-11-10 20:36:49 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:37:43 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:36:58s. Time for last 1,000,000: 53s. Last read position: chr6:4,126,386 INFO 2016-11-10 20:37:43 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:41:54 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:41:09s. Time for last 1,000,000: 251s. Last read position: chr6:28,666,579 INFO 2016-11-10 20:41:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:45:09 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:44:24s. Time for last 1,000,000: 194s. Last read position: chr6:49,527,281 INFO 2016-11-10 20:45:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:46:52 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:46:07s. Time for last 1,000,000: 103s. Last read position: chr6:81,728,195 INFO 2016-11-10 20:46:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:51:14 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:50:29s. Time for last 1,000,000: 261s. Last read position: chr6:107,535,760 INFO 2016-11-10 20:51:14 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:53:01 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:52:16s. Time for last 1,000,000: 106s. Last read position: chr6:132,364,408 INFO 2016-11-10 20:53:01 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:54:32 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:53:47s. Time for last 1,000,000: 91s. Last read position: chr6:156,918,595 INFO 2016-11-10 20:54:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:58:42 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:57:57s. Time for last 1,000,000: 250s. Last read position: chr7:18,636,743 INFO 2016-11-10 20:58:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:01:14 MarkDuplicates Read 42,000,000 records. Elapsed time: 01:00:29s. Time for last 1,000,000: 152s. Last read position: chr7:53,850,313 INFO 2016-11-10 21:01:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:02:45 MarkDuplicates Read 43,000,000 records. Elapsed time: 01:02:01s. Time for last 1,000,000: 91s. Last read position: chr7:96,503,433 INFO 2016-11-10 21:02:45 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:15:20 MarkDuplicates Read 44,000,000 records. Elapsed time: 01:14:36s. Time for last 1,000,000: 754s. Last read position: chr7:120,651,846 INFO 2016-11-10 21:15:20 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:28:42 MarkDuplicates Read 45,000,000 records. Elapsed time: 01:27:57s. Time for last 1,000,000: 801s. Last read position: chr7:146,401,497 INFO 2016-11-10 21:28:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:31:09 MarkDuplicates Read 46,000,000 records. Elapsed time: 01:30:25s. Time for last 1,000,000: 147s. Last read position: chr8:17,030,519 INFO 2016-11-10 21:31:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:35:12 MarkDuplicates Read 47,000,000 records. Elapsed time: 01:34:28s. Time for last 1,000,000: 242s. Last read position: chr8:42,750,671 INFO 2016-11-10 21:35:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:36:06 MarkDuplicates Read 48,000,000 records. Elapsed time: 01:35:21s. Time for last 1,000,000: 53s. Last read position: chr8:85,385,487 INFO 2016-11-10 21:36:06 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:37:28 MarkDuplicates Read 49,000,000 records. Elapsed time: 01:36:43s. Time for last 1,000,000: 82s. Last read position: chr8:124,358,985 INFO 2016-11-10 21:37:28 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:39:41 MarkDuplicates Read 50,000,000 records. Elapsed time: 01:38:57s. Time for last 1,000,000: 133s. Last read position: chr9:18,183,883 INFO 2016-11-10 21:39:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:44:06 MarkDuplicates Read 51,000,000 records. Elapsed time: 01:43:22s. Time for last 1,000,000: 264s. Last read position: chr9:84,163,983 INFO 2016-11-10 21:44:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:46:39 MarkDuplicates Read 52,000,000 records. Elapsed time: 01:45:54s. Time for last 1,000,000: 152s. Last read position: chr9:119,875,535 INFO 2016-11-10 21:46:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:49:27 MarkDuplicates Read 53,000,000 records. Elapsed time: 01:48:43s. Time for last 1,000,000: 168s. Last read position: chr10:5,661,683 INFO 2016-11-10 21:49:27 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 21:50:09 MarkDuplicates Read 54,000,000 records. Elapsed time: 01:49:24s. Time for last 1,000,000: 41s. Last read position: chr10:29,748,948 INFO 2016-11-10 21:50:09 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:51:50 MarkDuplicates Read 55,000,000 records. Elapsed time: 01:51:06s. Time for last 1,000,000: 101s. Last read position: chr10:61,280,221 INFO 2016-11-10 21:51:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:52:33 MarkDuplicates Read 56,000,000 records. Elapsed time: 01:51:49s. Time for last 1,000,000: 43s. Last read position: chr10:85,305,552 INFO 2016-11-10 21:52:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:52:45 MarkDuplicates Read 57,000,000 records. Elapsed time: 01:52:00s. Time for last 1,000,000: 11s. Last read position: chr10:108,129,202 INFO 2016-11-10 21:52:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:54:51 MarkDuplicates Read 58,000,000 records. Elapsed time: 01:54:06s. Time for last 1,000,000: 126s. Last read position: chr10:132,730,123 INFO 2016-11-10 21:54:51 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:55:08 MarkDuplicates Read 59,000,000 records. Elapsed time: 01:54:23s. Time for last 1,000,000: 17s. Last read position: chr11:35,359,267 INFO 2016-11-10 21:55:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:56:15 MarkDuplicates Read 60,000,000 records. Elapsed time: 01:55:30s. Time for last 1,000,000: 66s. Last read position: chr11:75,696,431 INFO 2016-11-10 21:56:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:56:29 MarkDuplicates Read 61,000,000 records. Elapsed time: 01:55:44s. Time for last 1,000,000: 13s. Last read position: chr11:114,414,621 INFO 2016-11-10 21:56:29 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 21:56:54 MarkDuplicates Read 62,000,000 records. Elapsed time: 01:56:09s. Time for last 1,000,000: 25s. Last read position: chr12:8,900,276 INFO 2016-11-10 21:56:54 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 21:57:45 MarkDuplicates Read 63,000,000 records. Elapsed time: 01:57:00s. Time for last 1,000,000: 50s. Last read position: chr12:38,863,889 INFO 2016-11-10 21:57:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:58:19 MarkDuplicates Read 64,000,000 records. Elapsed time: 01:57:35s. Time for last 1,000,000: 34s. Last read position: chr12:60,598,824 INFO 2016-11-10 21:58:19 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:59:58 MarkDuplicates Read 65,000,000 records. Elapsed time: 01:59:14s. Time for last 1,000,000: 98s. Last read position: chr12:88,520,538 INFO 2016-11-10 21:59:58 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 22:06:21 MarkDuplicates Read 66,000,000 records. Elapsed time: 02:05:36s. Time for last 1,000,000: 382s. Last read position: chr12:112,268,437 INFO 2016-11-10 22:06:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:09:48 MarkDuplicates Read 67,000,000 records. Elapsed time: 02:09:03s. Time for last 1,000,000: 207s. Last read position: chr13:23,999,632 INFO 2016-11-10 22:09:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:10:08 MarkDuplicates Read 68,000,000 records. Elapsed time: 02:09:23s. Time for last 1,000,000: 19s. Last read position: chr13:51,165,870 INFO 2016-11-10 22:10:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:10:32 MarkDuplicates Read 69,000,000 records. Elapsed time: 02:09:47s. Time for last 1,000,000: 24s. Last read position: chr13:88,986,369 INFO 2016-11-10 22:10:32 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:15:12 MarkDuplicates Read 70,000,000 records. Elapsed time: 02:14:27s. Time for last 1,000,000: 279s. Last read position: chr14:23,149,367 INFO 2016-11-10 22:15:12 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 22:15:56 MarkDuplicates Read 71,000,000 records. Elapsed time: 02:15:12s. Time for last 1,000,000: 44s. Last read position: chr14:58,140,905 INFO 2016-11-10 22:15:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:16:17 MarkDuplicates Read 72,000,000 records. Elapsed time: 02:15:32s. Time for last 1,000,000: 20s. Last read position: chr14:91,912,553 INFO 2016-11-10 22:16:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:16:52 MarkDuplicates Read 73,000,000 records. Elapsed time: 02:16:07s. Time for last 1,000,000: 34s. Last read position: chr15:38,895,095 INFO 2016-11-10 22:16:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:20:21 MarkDuplicates Read 74,000,000 records. Elapsed time: 02:19:36s. Time for last 1,000,000: 208s. Last read position: chr15:68,188,367 INFO 2016-11-10 22:20:21 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 22:20:37 MarkDuplicates Read 75,000,000 records. Elapsed time: 02:19:52s. Time for last 1,000,000: 15s. Last read position: chr15:87,921,272 INFO 2016-11-10 22:20:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:20:49 MarkDuplicates Read 76,000,000 records. Elapsed time: 02:20:04s. Time for last 1,000,000: 12s. Last read position: chr16:11,143,813 INFO 2016-11-10 22:20:49 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:21:01 MarkDuplicates Read 77,000,000 records. Elapsed time: 02:20:16s. Time for last 1,000,000: 11s. Last read position: chr16:51,391,437 INFO 2016-11-10 22:21:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:21:16 MarkDuplicates Read 78,000,000 records. Elapsed time: 02:20:31s. Time for last 1,000,000: 15s. Last read position: chr16:84,928,458 INFO 2016-11-10 22:21:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:23:17 MarkDuplicates Read 79,000,000 records. Elapsed time: 02:22:32s. Time for last 1,000,000: 121s. Last read position: chr17:18,368,935 INFO 2016-11-10 22:23:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:33:07 MarkDuplicates Read 80,000,000 records. Elapsed time: 02:32:22s. Time for last 1,000,000: 590s. Last read position: chr17:44,246,522 INFO 2016-11-10 22:33:07 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:40:02 MarkDuplicates Read 81,000,000 records. Elapsed time: 02:39:17s. Time for last 1,000,000: 414s. Last read position: chr17:66,172,158 INFO 2016-11-10 22:40:02 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 22:48:48 MarkDuplicates Read 82,000,000 records. Elapsed time: 02:48:03s. Time for last 1,000,000: 525s. Last read position: chr18:5,619,614 INFO 2016-11-10 22:48:48 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:55:02 MarkDuplicates Read 83,000,000 records. Elapsed time: 02:54:18s. Time for last 1,000,000: 374s. Last read position: chr18:46,152,631 INFO 2016-11-10 22:55:02 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:00:39 MarkDuplicates Read 84,000,000 records. Elapsed time: 02:59:54s. Time for last 1,000,000: 336s. Last read position: chr19:1,328,731 INFO 2016-11-10 23:00:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:04:53 MarkDuplicates Read 85,000,000 records. Elapsed time: 03:04:08s. Time for last 1,000,000: 253s. Last read position: chr19:28,148,444 INFO 2016-11-10 23:04:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:07:44 MarkDuplicates Read 86,000,000 records. Elapsed time: 03:06:59s. Time for last 1,000,000: 170s. Last read position: chr19:40,341,579 INFO 2016-11-10 23:07:44 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 23:10:36 MarkDuplicates Read 87,000,000 records. Elapsed time: 03:09:51s. Time for last 1,000,000: 172s. Last read position: chr20:3,222,035 INFO 2016-11-10 23:10:36 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:13:03 MarkDuplicates Read 88,000,000 records. Elapsed time: 03:12:18s. Time for last 1,000,000: 146s. Last read position: chr20:37,218,903 INFO 2016-11-10 23:13:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:24:37 MarkDuplicates Read 89,000,000 records. Elapsed time: 03:23:52s. Time for last 1,000,000: 693s. Last read position: chr20:62,871,367 INFO 2016-11-10 23:24:37 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 23:25:05 MarkDuplicates Read 90,000,000 records. Elapsed time: 03:24:21s. Time for last 1,000,000: 28s. Last read position: chr21:39,474,524 INFO 2016-11-10 23:25:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:26:56 MarkDuplicates Read 91,000,000 records. Elapsed time: 03:26:11s. Time for last 1,000,000: 110s. Last read position: chr22:31,346,944 INFO 2016-11-10 23:26:56 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 23:28:15 MarkDuplicates Read 92,000,000 records. Elapsed time: 03:27:30s. Time for last 1,000,000: 78s. Last read position: chrX:6,235,951 INFO 2016-11-10 23:28:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:29:22 MarkDuplicates Read 93,000,000 records. Elapsed time: 03:28:37s. Time for last 1,000,000: 67s. Last read position: chrX:38,820,975 INFO 2016-11-10 23:29:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:31:44 MarkDuplicates Read 94,000,000 records. Elapsed time: 03:31:00s. Time for last 1,000,000: 142s. Last read position: chrX:69,473,954 INFO 2016-11-10 23:31:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:32:30 MarkDuplicates Read 95,000,000 records. Elapsed time: 03:31:46s. Time for last 1,000,000: 46s. Last read position: chrX:92,683,143 INFO 2016-11-10 23:32:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:32:47 MarkDuplicates Read 96,000,000 records. Elapsed time: 03:32:02s. Time for last 1,000,000: 16s. Last read position: chrX:118,447,518 INFO 2016-11-10 23:32:47 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 23:33:03 MarkDuplicates Read 97,000,000 records. Elapsed time: 03:32:18s. Time for last 1,000,000: 16s. Last read position: chrX:142,819,613 INFO 2016-11-10 23:33:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:33:15 MarkDuplicates Read 98,000,000 records. Elapsed time: 03:32:31s. Time for last 1,000,000: 12s. Last read position: chrM:3,995 INFO 2016-11-10 23:33:15 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM. INFO 2016-11-10 23:33:34 MarkDuplicates Read 99,000,000 records. Elapsed time: 03:32:49s. Time for last 1,000,000: 18s. Last read position: chrM:11,775 INFO 2016-11-10 23:33:34 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM. INFO 2016-11-10 23:33:58 MarkDuplicates Read 99989486 records. 0 pairs never matched. INFO 2016-11-10 23:34:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 5823819248; totalMemory: 5905055744; maxMemory: 11453595648 INFO 2016-11-10 23:34:18 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-10 23:34:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-10 23:37:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-10 23:39:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-10 23:39:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 5611635792; totalMemory: 8553758720; maxMemory: 11453595648 INFO 2016-11-10 23:39:19 MarkDuplicates Marking 496224 records as duplicates. INFO 2016-11-10 23:39:19 MarkDuplicates Found 42648 optical duplicate clusters. INFO 2016-11-11 01:16:54 MarkDuplicates Written 10,000,000 records. Elapsed time: 01:36:42s. Time for last 10,000,000: 5,802s. Last read position: chr2:3,652,468 INFO 2016-11-11 02:27:12 MarkDuplicates Written 20,000,000 records. Elapsed time: 02:47:01s. Time for last 10,000,000: 4,218s. Last read position: chr3:128,121,129 INFO 2016-11-11 04:25:04 MarkDuplicates Written 30,000,000 records. Elapsed time: 04:44:52s. Time for last 10,000,000: 7,071s. Last read position: chr5:86,336,676 INFO 2016-11-11 05:04:01 MarkDuplicates Written 40,000,000 records. Elapsed time: 05:23:50s. Time for last 10,000,000: 2,337s. Last read position: chr6:156,918,595 INFO 2016-11-11 05:34:22 MarkDuplicates Written 50,000,000 records. Elapsed time: 05:54:11s. Time for last 10,000,000: 1,821s. Last read position: chr9:18,183,883 INFO 2016-11-11 05:50:16 MarkDuplicates Written 60,000,000 records. Elapsed time: 06:10:04s. Time for last 10,000,000: 953s. Last read position: chr11:75,696,431 INFO 2016-11-11 06:18:17 MarkDuplicates Written 70,000,000 records. Elapsed time: 06:38:05s. Time for last 10,000,000: 1,680s. Last read position: chr14:23,149,367 INFO 2016-11-11 06:40:12 MarkDuplicates Written 80,000,000 records. Elapsed time: 07:00:00s. Time for last 10,000,000: 1,314s. Last read position: chr17:44,246,522 INFO 2016-11-11 06:57:04 MarkDuplicates Written 90,000,000 records. Elapsed time: 07:16:53s. Time for last 10,000,000: 1,012s. Last read position: chr21:39,474,524 INFO 2016-11-11 07:03:59 MarkDuplicates Before output close freeMemory: 8663711216; totalMemory: 8747745280; maxMemory: 11453595648 INFO 2016-11-11 07:04:00 MarkDuplicates After output close freeMemory: 8664232608; totalMemory: 8748269568; maxMemory: 11453595648 [Fri Nov 11 07:04:00 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 663.34 minutes. Runtime.totalMemory()=8748269568 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/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/SRR1370902_1/out/align/rep1/SRR1370902_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370902_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_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
--------------------Stdout-------------------- 12095 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.11 sec [bwa_aln_core] refine gapped alignments... 1.16 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 0.43 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.59 sec [bwa_aln_core] refine gapped alignments... 0.84 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.35 sec [bwa_aln_core] refine gapped alignments... 10.17 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.61 sec [bwa_aln_core] refine gapped alignments... 3.00 sec [bwa_aln_core] print alignments... 0.69 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 53.45 sec [bwa_aln_core] refine gapped alignments... 7.23 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 38.21 sec [bwa_aln_core] refine gapped alignments... 6.98 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.37 sec [bwa_aln_core] refine gapped alignments... 8.68 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.38 sec [bwa_aln_core] refine gapped alignments... 2.03 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.45 sec [bwa_aln_core] refine gapped alignments... 8.59 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.28 sec [bwa_aln_core] refine gapped alignments... 9.69 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.23 sec [bwa_aln_core] refine gapped alignments... 5.89 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.27 sec [bwa_aln_core] refine gapped alignments... 6.84 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.26 sec [bwa_aln_core] refine gapped alignments... 7.19 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.58 sec [bwa_aln_core] refine gapped alignments... 2.40 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.09 sec [bwa_aln_core] refine gapped alignments... 4.92 sec [bwa_aln_core] print alignments... 0.69 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.81 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.98 sec [bwa_aln_core] refine gapped alignments... 10.89 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.25 sec [bwa_aln_core] refine gapped alignments... 0.87 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.34 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.10 sec [bwa_aln_core] refine gapped alignments... 1.01 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.41 sec [bwa_aln_core] refine gapped alignments... 1.46 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.56 sec [bwa_aln_core] refine gapped alignments... 5.95 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.36 sec [bwa_aln_core] refine gapped alignments... 5.14 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.96 sec [bwa_aln_core] refine gapped alignments... 4.81 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.35 sec [bwa_aln_core] refine gapped alignments... 5.23 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.45 sec [bwa_aln_core] refine gapped alignments... 3.33 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.74 sec [bwa_aln_core] refine gapped alignments... 3.43 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.98 sec [bwa_aln_core] refine gapped alignments... 3.71 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.36 sec [bwa_aln_core] refine gapped alignments... 6.53 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.72 sec [bwa_aln_core] refine gapped alignments... 5.17 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.63 sec [bwa_aln_core] refine gapped alignments... 4.31 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.71 sec [bwa_aln_core] refine gapped alignments... 6.91 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.14 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.51 sec [bwa_aln_core] refine gapped alignments... 4.43 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.71 sec [bwa_aln_core] refine gapped alignments... 1.40 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.38 sec [bwa_aln_core] refine gapped alignments... 7.06 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 38.82 sec [bwa_aln_core] refine gapped alignments... 8.13 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.18 sec [bwa_aln_core] refine gapped alignments... 9.03 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.11 sec [bwa_aln_core] refine gapped alignments... 9.22 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 50.30 sec [bwa_aln_core] refine gapped alignments... 12.77 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.70 sec [bwa_aln_core] refine gapped alignments... 0.84 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.28 sec [bwa_aln_core] refine gapped alignments... 7.94 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.36 sec [bwa_aln_core] refine gapped alignments... 5.12 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.98 sec [bwa_aln_core] refine gapped alignments... 5.54 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 58.70 sec [bwa_aln_core] refine gapped alignments... 5.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.82 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.96 sec [bwa_aln_core] refine gapped alignments... 4.71 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.94 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.40 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.92 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.77 sec [bwa_aln_core] refine gapped alignments... 1.36 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.73 sec [bwa_aln_core] refine gapped alignments... 6.50 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.01 sec [bwa_aln_core] refine gapped alignments... 2.59 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.04 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.75 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.11 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.18 sec [bwa_aln_core] refine gapped alignments... 1.30 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.20 sec [bwa_aln_core] refine gapped alignments... 5.89 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.35 sec [bwa_aln_core] refine gapped alignments... 3.13 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.20 sec [bwa_aln_core] refine gapped alignments... 5.67 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.59 sec [bwa_aln_core] refine gapped alignments... 7.63 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.26 sec [bwa_aln_core] refine gapped alignments... 0.87 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.14 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.08 sec [bwa_aln_core] refine gapped alignments... 10.07 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.84 sec [bwa_aln_core] refine gapped alignments... 1.76 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.74 sec [bwa_aln_core] refine gapped alignments... 6.61 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.22 sec [bwa_aln_core] refine gapped alignments... 3.77 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.98 sec [bwa_aln_core] refine gapped alignments... 8.81 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.08 sec [bwa_aln_core] refine gapped alignments... 6.95 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.64 sec [bwa_aln_core] refine gapped alignments... 5.99 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.52 sec [bwa_aln_core] refine gapped alignments... 6.32 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.90 sec [bwa_aln_core] refine gapped alignments... 8.70 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.31 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.86 sec [bwa_aln_core] refine gapped alignments... 0.83 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.13 sec [bwa_aln_core] refine gapped alignments... 5.89 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.48 sec [bwa_aln_core] refine gapped alignments... 6.56 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.46 sec [bwa_aln_core] refine gapped alignments... 6.15 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.12 sec [bwa_aln_core] refine gapped alignments... 4.85 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.07 sec [bwa_aln_core] refine gapped alignments... 5.99 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.75 sec [bwa_aln_core] refine gapped alignments... 6.65 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.73 sec [bwa_aln_core] refine gapped alignments... 5.27 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.12 sec [bwa_aln_core] refine gapped alignments... 6.51 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.02 sec [bwa_aln_core] refine gapped alignments... 8.36 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.12 sec [bwa_aln_core] refine gapped alignments... 6.63 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.83 sec [bwa_aln_core] refine gapped alignments... 9.74 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.77 sec [bwa_aln_core] refine gapped alignments... 4.29 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 38.01 sec [bwa_aln_core] refine gapped alignments... 6.68 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.91 sec [bwa_aln_core] refine gapped alignments... 0.86 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.17 sec [bwa_aln_core] refine gapped alignments... 6.62 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.69 sec [bwa_aln_core] refine gapped alignments... 0.93 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.65 sec [bwa_aln_core] refine gapped alignments... 8.57 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 23662830 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370902_1.fastq.gz [main] Real time: 4004.076 sec; CPU: 3798.876 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 7180 (process ID) old priority 0, new priority 10 |
| Type | Name | Value |
|---|---|---|
| int{} | filesize | {rep1=4531736640, ctl1=11033042636} |
| int{} | nth_rep | {rep1=1, ctl1=4} |