| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161113_130759_255 |
| Start time | 2016-11-13 13:07:59 |
| Run time | 07:25:07.098 |
| Tasks executed | 9 |
| Tasks failed | 1 |
| Tasks failed names | dedup_bam_2 rep1 |
| Arguments* | [-title, SRR1370888_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370888_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 | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_42 | thread_Root | chipseq.bds.20161113_130759_255_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161113_130759_255_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 chipseq.bds.20161113_130759_255_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_14 chipseq.bds.20161113_130759_255_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_16 |
| thread_41 | thread_Root | chipseq.bds.20161113_130759_255_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11 chipseq.bds.20161113_130759_255_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 chipseq.bds.20161113_130759_255_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_15 chipseq.bds.20161113_130759_255_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_17 chipseq.bds.20161113_130759_255_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_18 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_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/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_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/SRR1370888_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-------------------- 18380 (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/SRR1370888_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_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-------------------- 10257 (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] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.80 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... 32.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.90 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.22 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.39 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.49 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.89 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.42 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.46 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.29 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.07 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.51 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... 31.13 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... 31.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.05 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.76 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.28 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.33 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... 30.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.45 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.72 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.14 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.41 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.77 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.30 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.68 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.56 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.94 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.53 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.87 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.29 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.78 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.83 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.20 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... 31.02 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... 31.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.84 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... 35.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.81 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.64 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.06 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 24.77 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 21339482 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/SRR1370888_1.fastq.gz [main] Real time: 2839.610 sec; CPU: 2819.232 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/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_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/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_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-------------------- 45608 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Sun Nov 13 15:35:21 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_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 [Sun Nov 13 15:35:21 PST 2016] Executing as imk1@surya 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 2016-11-13 15:35:21 MarkDuplicates Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-13 15:35:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-13 15:35:21 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-13 15:35:30 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 8s. Last read position: chr1:22,298,551 INFO 2016-11-13 15:35:30 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:35:37 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 6s. Last read position: chr1:41,895,424 INFO 2016-11-13 15:35:37 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:35:43 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 5s. Last read position: chr1:63,396,527 INFO 2016-11-13 15:35:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:35:50 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 7s. Last read position: chr1:89,147,707 INFO 2016-11-13 15:35:50 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:35:55 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 5s. Last read position: chr1:115,615,553 INFO 2016-11-13 15:35:55 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:36:04 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 8s. Last read position: chr1:164,468,682 INFO 2016-11-13 15:36:04 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:36:11 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 7s. Last read position: chr1:189,102,252 INFO 2016-11-13 15:36:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:36:24 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 12s. Last read position: chr1:213,979,760 INFO 2016-11-13 15:36:24 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:36:31 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 7s. Last read position: chr1:231,814,268 INFO 2016-11-13 15:36:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:36:45 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 14s. Last read position: chr2:3,652,468 INFO 2016-11-13 15:36:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:36:49 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: chr2:39,505,122 INFO 2016-11-13 15:36:49 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:36:58 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 8s. Last read position: chr2:73,561,393 INFO 2016-11-13 15:36:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:37:08 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 10s. Last read position: chr2:120,526,571 INFO 2016-11-13 15:37:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:37:20 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 11s. Last read position: chr2:160,316,783 INFO 2016-11-13 15:37:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:37:25 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 5s. Last read position: chr2:195,549,735 INFO 2016-11-13 15:37:25 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:37:31 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 5s. Last read position: chr2:230,358,034 INFO 2016-11-13 15:37:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:37:37 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 6s. Last read position: chr3:16,305,780 INFO 2016-11-13 15:37:37 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:37:42 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 4s. Last read position: chr3:49,251,279 INFO 2016-11-13 15:37:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:37:53 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 11s. Last read position: chr3:84,621,225 INFO 2016-11-13 15:37:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:37:58 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 5s. Last read position: chr3:128,121,129 INFO 2016-11-13 15:37:58 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:38:05 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 6s. Last read position: chr3:165,373,238 INFO 2016-11-13 15:38:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:38:10 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 5s. Last read position: chr3:195,333,247 INFO 2016-11-13 15:38:10 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:38:16 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 6s. Last read position: chr4:37,752,582 INFO 2016-11-13 15:38:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:38:28 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 11s. Last read position: chr4:81,286,306 INFO 2016-11-13 15:38:28 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:38:35 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 6s. Last read position: chr4:119,339,736 INFO 2016-11-13 15:38:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:38:40 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 5s. Last read position: chr4:158,818,783 INFO 2016-11-13 15:38:40 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:38:47 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 6s. Last read position: chr5:6,447,551 INFO 2016-11-13 15:38:47 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-11-13 15:38:53 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 5s. Last read position: chr5:33,219,021 INFO 2016-11-13 15:38:53 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:39:04 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 11s. Last read position: chr5:60,694,078 INFO 2016-11-13 15:39:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:39:10 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 6s. Last read position: chr5:86,336,676 INFO 2016-11-13 15:39:10 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:39:16 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 5s. Last read position: chr5:112,930,184 INFO 2016-11-13 15:39:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:39:23 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 7s. Last read position: chr5:136,852,889 INFO 2016-11-13 15:39:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:39:31 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 7s. Last read position: chr5:160,271,193 INFO 2016-11-13 15:39:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:39:35 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 4s. Last read position: chr6:4,126,386 INFO 2016-11-13 15:39:35 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:39:48 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 13s. Last read position: chr6:28,666,579 INFO 2016-11-13 15:39:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:39:55 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 6s. Last read position: chr6:49,527,281 INFO 2016-11-13 15:39:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:40:02 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 7s. Last read position: chr6:81,728,195 INFO 2016-11-13 15:40:02 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:07 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 5s. Last read position: chr6:107,535,760 INFO 2016-11-13 15:40:07 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:15 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 7s. Last read position: chr6:132,364,408 INFO 2016-11-13 15:40:15 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:40:30 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 14s. Last read position: chr6:156,918,595 INFO 2016-11-13 15:40:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:35 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 5s. Last read position: chr7:18,636,743 INFO 2016-11-13 15:40:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:40:41 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 5s. Last read position: chr7:53,850,313 INFO 2016-11-13 15:40:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:40:48 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 7s. Last read position: chr7:96,503,433 INFO 2016-11-13 15:40:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:55 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 6s. Last read position: chr7:120,651,846 INFO 2016-11-13 15:40:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:42:01 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 65s. Last read position: chr7:146,401,497 INFO 2016-11-13 15:42:01 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:42:09 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 7s. Last read position: chr8:17,030,519 INFO 2016-11-13 15:42:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:42:16 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 7s. Last read position: chr8:42,750,671 INFO 2016-11-13 15:42:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:42:28 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 11s. Last read position: chr8:85,385,487 INFO 2016-11-13 15:42:28 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:42:33 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 4s. Last read position: chr8:124,358,985 INFO 2016-11-13 15:42:33 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:42:38 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 4s. Last read position: chr9:18,183,883 INFO 2016-11-13 15:42:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:42:44 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 6s. Last read position: chr9:84,163,983 INFO 2016-11-13 15:42:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:42:50 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 5s. Last read position: chr9:119,875,535 INFO 2016-11-13 15:42:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:42:55 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 4s. Last read position: chr10:5,661,683 INFO 2016-11-13 15:42:55 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:43:01 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 5s. Last read position: chr10:29,748,948 INFO 2016-11-13 15:43:01 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:43:10 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 9s. Last read position: chr10:61,280,221 INFO 2016-11-13 15:43:10 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:43:17 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 6s. Last read position: chr10:85,305,552 INFO 2016-11-13 15:43:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:43:22 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 4s. Last read position: chr10:108,129,202 INFO 2016-11-13 15:43:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:43:28 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 5s. Last read position: chr10:132,730,123 INFO 2016-11-13 15:43:28 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:43:35 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 7s. Last read position: chr11:35,359,267 INFO 2016-11-13 15:43:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:43:45 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 9s. Last read position: chr11:75,696,431 INFO 2016-11-13 15:43:45 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:43:51 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 6s. Last read position: chr11:114,414,621 INFO 2016-11-13 15:43:51 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:44:05 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 14s. Last read position: chr12:8,900,276 INFO 2016-11-13 15:44:05 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:44:11 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 6s. Last read position: chr12:38,863,889 INFO 2016-11-13 15:44:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:44:20 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 8s. Last read position: chr12:60,598,824 INFO 2016-11-13 15:44:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:44:24 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 4s. Last read position: chr12:88,520,538 INFO 2016-11-13 15:44:24 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:44:30 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 6s. Last read position: chr12:112,268,437 INFO 2016-11-13 15:44:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:44:37 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 6s. Last read position: chr13:23,999,632 INFO 2016-11-13 15:44:37 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:44:45 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 7s. Last read position: chr13:51,165,870 INFO 2016-11-13 15:44:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:44:50 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 4s. Last read position: chr13:88,986,369 INFO 2016-11-13 15:44:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:45:07 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 17s. Last read position: chr14:23,149,367 INFO 2016-11-13 15:45:07 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:45:15 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 8s. Last read position: chr14:58,140,905 INFO 2016-11-13 15:45:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:45:23 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 8s. Last read position: chr14:91,912,553 INFO 2016-11-13 15:45:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:45:29 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 5s. Last read position: chr15:38,895,095 INFO 2016-11-13 15:45:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:45:38 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 8s. Last read position: chr15:68,188,367 INFO 2016-11-13 15:45:38 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:45:47 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 9s. Last read position: chr15:87,921,272 INFO 2016-11-13 15:45:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:45:54 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 6s. Last read position: chr16:11,143,813 INFO 2016-11-13 15:45:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:46:00 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 6s. Last read position: chr16:51,391,437 INFO 2016-11-13 15:46:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:46:17 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 16s. Last read position: chr16:84,928,458 INFO 2016-11-13 15:46:17 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:46:22 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 5s. Last read position: chr17:18,368,935 INFO 2016-11-13 15:46:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:46:30 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 7s. Last read position: chr17:44,246,522 INFO 2016-11-13 15:46:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:46:35 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 5s. Last read position: chr17:66,172,158 INFO 2016-11-13 15:46:35 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-13 15:46:43 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 7s. Last read position: chr18:5,619,614 INFO 2016-11-13 15:46:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:46:52 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 9s. Last read position: chr18:46,152,631 INFO 2016-11-13 15:46:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:46:56 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 4s. Last read position: chr19:1,328,731 INFO 2016-11-13 15:46:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:47:05 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 8s. Last read position: chr19:28,148,444 INFO 2016-11-13 15:47:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:47:22 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 16s. Last read position: chr19:40,341,579 INFO 2016-11-13 15:47:22 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:47:28 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 6s. Last read position: chr20:3,222,035 INFO 2016-11-13 15:47:28 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:47:35 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 7s. Last read position: chr20:37,218,903 INFO 2016-11-13 15:47:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:48:35 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 59s. Last read position: chr20:62,871,367 INFO 2016-11-13 15:48:35 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-13 15:48:44 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 9s. Last read position: chr21:39,474,524 INFO 2016-11-13 15:48:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:48:51 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 6s. Last read position: chr22:31,346,944 INFO 2016-11-13 15:48:51 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:49:01 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 10s. Last read position: chrX:6,235,951 INFO 2016-11-13 15:49:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:49:11 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 9s. Last read position: chrX:38,820,975 INFO 2016-11-13 15:49:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:49:18 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 7s. Last read position: chrX:69,473,954 INFO 2016-11-13 15:49:18 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:49:27 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 8s. Last read position: chrX:92,683,143 INFO 2016-11-13 15:49:27 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:49:31 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 4s. Last read position: chrX:118,447,518 INFO 2016-11-13 15:49:31 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:49:38 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 6s. Last read position: chrX:142,819,613 INFO 2016-11-13 15:49:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:49:48 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 9s. Last read position: chrM:3,995 INFO 2016-11-13 15:49:48 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM. INFO 2016-11-13 15:49:52 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 4s. Last read position: chrM:11,775 INFO 2016-11-13 15:49:52 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM. INFO 2016-11-13 15:50:00 MarkDuplicates Read 99989486 records. 0 pairs never matched. INFO 2016-11-13 15:50:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 6211101248; totalMemory: 6289358848; maxMemory: 11453595648 INFO 2016-11-13 15:50:11 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-13 15:50:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-13 15:50:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-13 15:50:53 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-13 15:50:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 6194740872; totalMemory: 9134669824; maxMemory: 11453595648 INFO 2016-11-13 15:50:54 MarkDuplicates Marking 496224 records as duplicates. INFO 2016-11-13 15:50:54 MarkDuplicates Found 42648 optical duplicate clusters. INFO 2016-11-13 15:53:13 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:10s. Time for last 10,000,000: 130s. Last read position: chr2:3,652,468 INFO 2016-11-13 15:55:55 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:04:52s. Time for last 10,000,000: 161s. Last read position: chr3:128,121,129 INFO 2016-11-13 15:58:35 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:07:32s. Time for last 10,000,000: 159s. Last read position: chr5:86,336,676 INFO 2016-11-13 16:01:14 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:10:11s. Time for last 10,000,000: 158s. Last read position: chr6:156,918,595 INFO 2016-11-13 16:04:37 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:13:34s. Time for last 10,000,000: 203s. Last read position: chr9:18,183,883 INFO 2016-11-13 16:07:22 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:16:19s. Time for last 10,000,000: 164s. Last read position: chr11:75,696,431 INFO 2016-11-13 16:10:11 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:19:08s. Time for last 10,000,000: 169s. Last read position: chr14:23,149,367 INFO 2016-11-13 16:13:02 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:21:59s. Time for last 10,000,000: 170s. Last read position: chr17:44,246,522 INFO 2016-11-13 16:15:47 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:24:44s. Time for last 10,000,000: 164s. Last read position: chr21:39,474,524 INFO 2016-11-13 16:18:20 MarkDuplicates Before output close freeMemory: 9194118104; totalMemory: 9279897600; maxMemory: 11453595648 INFO 2016-11-13 16:18:20 MarkDuplicates After output close freeMemory: 9196665088; totalMemory: 9282519040; maxMemory: 11453595648 [Sun Nov 13 16:18:20 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 42.99 minutes. Runtime.totalMemory()=9282519040 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370888_1/out/align/rep1/SRR1370888_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370888_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_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-------------------- 2316 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.36 sec [bwa_aln_core] refine gapped alignments... 2.71 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 1.11 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.06 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 1.07 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.54 sec [bwa_aln_core] refine gapped alignments... 0.93 sec [bwa_aln_core] print alignments... 1.14 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.30 sec [bwa_aln_core] refine gapped alignments... 0.91 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.54 sec [bwa_aln_core] refine gapped alignments... 0.91 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.02 sec [bwa_aln_core] refine gapped alignments... 0.84 sec [bwa_aln_core] print alignments... 0.96 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.40 sec [bwa_aln_core] refine gapped alignments... 1.01 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.37 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 1.09 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.49 sec [bwa_aln_core] refine gapped alignments... 0.94 sec [bwa_aln_core] print alignments... 1.12 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.24 sec [bwa_aln_core] refine gapped alignments... 0.94 sec [bwa_aln_core] print alignments... 1.12 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.41 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 1.12 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.95 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... 1.03 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.95 sec [bwa_aln_core] refine gapped alignments... 0.83 sec [bwa_aln_core] print alignments... 0.94 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.63 sec [bwa_aln_core] refine gapped alignments... 1.03 sec [bwa_aln_core] print alignments... 1.10 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.34 sec [bwa_aln_core] refine gapped alignments... 0.93 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.07 sec [bwa_aln_core] refine gapped alignments... 4.14 sec [bwa_aln_core] print alignments... 1.15 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.92 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 1.11 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.95 sec [bwa_aln_core] refine gapped alignments... 1.36 sec [bwa_aln_core] print alignments... 1.07 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.80 sec [bwa_aln_core] refine gapped alignments... 0.89 sec [bwa_aln_core] print alignments... 1.03 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.63 sec [bwa_aln_core] refine gapped alignments... 0.99 sec [bwa_aln_core] print alignments... 1.29 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.95 sec [bwa_aln_core] refine gapped alignments... 1.10 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.61 sec [bwa_aln_core] refine gapped alignments... 0.89 sec [bwa_aln_core] print alignments... 0.95 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.92 sec [bwa_aln_core] refine gapped alignments... 2.19 sec [bwa_aln_core] print alignments... 0.86 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.74 sec [bwa_aln_core] refine gapped alignments... 1.84 sec [bwa_aln_core] print alignments... 1.09 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.57 sec [bwa_aln_core] refine gapped alignments... 0.88 sec [bwa_aln_core] print alignments... 0.97 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.84 sec [bwa_aln_core] refine gapped alignments... 0.89 sec [bwa_aln_core] print alignments... 0.87 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.40 sec [bwa_aln_core] refine gapped alignments... 1.04 sec [bwa_aln_core] print alignments... 0.85 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.75 sec [bwa_aln_core] refine gapped alignments... 0.86 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.32 sec [bwa_aln_core] refine gapped alignments... 0.83 sec [bwa_aln_core] print alignments... 0.96 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.52 sec [bwa_aln_core] refine gapped alignments... 0.84 sec [bwa_aln_core] print alignments... 1.04 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.86 sec [bwa_aln_core] refine gapped alignments... 0.86 sec [bwa_aln_core] print alignments... 0.96 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.33 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 1.08 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.66 sec [bwa_aln_core] refine gapped alignments... 0.79 sec [bwa_aln_core] print alignments... 0.93 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.97 sec [bwa_aln_core] refine gapped alignments... 0.86 sec [bwa_aln_core] print alignments... 1.14 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.53 sec [bwa_aln_core] refine gapped alignments... 0.77 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.81 sec [bwa_aln_core] refine gapped alignments... 0.77 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.26 sec [bwa_aln_core] refine gapped alignments... 2.90 sec [bwa_aln_core] print alignments... 1.12 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.74 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... 1.12 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.59 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.85 sec [bwa_aln_core] refine gapped alignments... 1.34 sec [bwa_aln_core] print alignments... 0.82 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.28 sec [bwa_aln_core] refine gapped alignments... 0.81 sec [bwa_aln_core] print alignments... 1.03 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.83 sec [bwa_aln_core] refine gapped alignments... 0.79 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.61 sec [bwa_aln_core] refine gapped alignments... 0.78 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.22 sec [bwa_aln_core] refine gapped alignments... 0.81 sec [bwa_aln_core] print alignments... 0.95 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.09 sec [bwa_aln_core] refine gapped alignments... 1.37 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.78 sec [bwa_aln_core] refine gapped alignments... 0.84 sec [bwa_aln_core] print alignments... 1.08 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.26 sec [bwa_aln_core] refine gapped alignments... 0.76 sec [bwa_aln_core] print alignments... 1.00 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.23 sec [bwa_aln_core] refine gapped alignments... 2.09 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.56 sec [bwa_aln_core] refine gapped alignments... 1.58 sec [bwa_aln_core] print alignments... 1.07 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.50 sec [bwa_aln_core] refine gapped alignments... 0.89 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.18 sec [bwa_aln_core] refine gapped alignments... 1.71 sec [bwa_aln_core] print alignments... 1.07 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.66 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... 0.94 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.43 sec [bwa_aln_core] refine gapped alignments... 1.25 sec [bwa_aln_core] print alignments... 0.95 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.56 sec [bwa_aln_core] refine gapped alignments... 0.95 sec [bwa_aln_core] print alignments... 0.85 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.35 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.05 sec [bwa_aln_core] refine gapped alignments... 2.54 sec [bwa_aln_core] print alignments... 1.17 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.70 sec [bwa_aln_core] refine gapped alignments... 0.82 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.22 sec [bwa_aln_core] refine gapped alignments... 2.76 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.28 sec [bwa_aln_core] refine gapped alignments... 0.83 sec [bwa_aln_core] print alignments... 1.01 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.11 sec [bwa_aln_core] refine gapped alignments... 0.77 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.56 sec [bwa_aln_core] refine gapped alignments... 3.16 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.12 sec [bwa_aln_core] refine gapped alignments... 0.81 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.09 sec [bwa_aln_core] refine gapped alignments... 0.81 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.62 sec [bwa_aln_core] refine gapped alignments... 1.38 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.19 sec [bwa_aln_core] refine gapped alignments... 1.76 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.96 sec [bwa_aln_core] refine gapped alignments... 2.22 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.76 sec [bwa_aln_core] refine gapped alignments... 2.41 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.70 sec [bwa_aln_core] refine gapped alignments... 2.28 sec [bwa_aln_core] print alignments... 0.93 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.00 sec [bwa_aln_core] refine gapped alignments... 2.56 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.83 sec [bwa_aln_core] refine gapped alignments... 1.51 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.61 sec [bwa_aln_core] refine gapped alignments... 0.93 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.16 sec [bwa_aln_core] refine gapped alignments... 1.69 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.78 sec [bwa_aln_core] refine gapped alignments... 1.39 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.53 sec [bwa_aln_core] refine gapped alignments... 1.79 sec [bwa_aln_core] print alignments... 1.09 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.63 sec [bwa_aln_core] refine gapped alignments... 1.82 sec [bwa_aln_core] print alignments... 1.28 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.75 sec [bwa_aln_core] refine gapped alignments... 2.79 sec [bwa_aln_core] print alignments... 1.12 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.85 sec [bwa_aln_core] refine gapped alignments... 3.24 sec [bwa_aln_core] print alignments... 0.97 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.36 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... 1.05 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.10 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.01 sec [bwa_aln_core] refine gapped alignments... 0.81 sec [bwa_aln_core] print alignments... 1.06 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.77 sec [bwa_aln_core] refine gapped alignments... 2.29 sec [bwa_aln_core] print alignments... 1.01 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.49 sec [bwa_aln_core] refine gapped alignments... 0.76 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 21339482 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/SRR1370888_1/out/align/rep1/SRR1370888_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370888_1.fastq.gz [main] Real time: 3388.020 sec; CPU: 1520.936 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 146
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 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 153
sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 155
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 1954 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370888_1/out/align/rep1/SRR1370888_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 548 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 507
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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 18219 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# 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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 27457 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Sun Nov 13 20:14:05 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.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 [Sun Nov 13 20:14:05 PST 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-13 20:14:05 MarkDuplicates Start of doWork freeMemory: 254879328; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-13 20:14:05 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-13 20:14:05 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-13 20:14:15 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr1:171,859,751 INFO 2016-11-13 20:14:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:21 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 6s. Last read position: chr2:80,188,275 INFO 2016-11-13 20:14:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:26 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 4s. Last read position: chr3:46,971,890 INFO 2016-11-13 20:14:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:29 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr4:53,526,131 INFO 2016-11-13 20:14:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:33 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 4s. Last read position: chr5:54,724,431 INFO 2016-11-13 20:14:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:38 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 5s. Last read position: chr6:18,811,956 INFO 2016-11-13 20:14:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:44 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 5s. Last read position: chr7:1,725,723 INFO 2016-11-13 20:14:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:48 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 4s. Last read position: chr8:29,716,585 INFO 2016-11-13 20:14:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:14:57 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 8s. Last read position: chr9:127,094,866 INFO 2016-11-13 20:14:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:00 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr11:6,722,073 INFO 2016-11-13 20:15:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:03 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr12:65,577,204 INFO 2016-11-13 20:15:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:13 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 10s. Last read position: chr13:104,354,750 INFO 2016-11-13 20:15:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:21 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 8s. Last read position: chr16:12,150,881 INFO 2016-11-13 20:15:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:24 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr18:27,572,413 INFO 2016-11-13 20:15:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:34 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 10s. Last read position: chr20:42,567,925 INFO 2016-11-13 20:15:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:37 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chrX:78,050,957 INFO 2016-11-13 20:15:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 20:15:39 MarkDuplicates Read 16668759 records. 0 pairs never matched. INFO 2016-11-13 20:15:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 4135771832; totalMemory: 5635571712; maxMemory: 11453595648 INFO 2016-11-13 20:15:46 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-13 20:15:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-13 20:15:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-13 20:15:48 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-13 20:15:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 2692565456; totalMemory: 5635571712; maxMemory: 11453595648 INFO 2016-11-13 20:15:50 MarkDuplicates Marking 680730 records as duplicates. INFO 2016-11-13 20:15:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-13 20:17:30 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 100s. Last read position: chr11:6,722,073 INFO 2016-11-13 20:18:32 MarkDuplicates Before output close freeMemory: 8296055400; totalMemory: 8377073664; maxMemory: 11453595648 INFO 2016-11-13 20:18:32 MarkDuplicates After output close freeMemory: 8420217392; totalMemory: 8501329920; maxMemory: 11453595648 [Sun Nov 13 20:18:32 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.45 minutes. Runtime.totalMemory()=8501329920 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 146
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 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
30767 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/chipseq.bds.20161113_130759_255_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_18.sh: line 15: sambamba: command not found
--------------------Post mortem info--------------------
==============================================================
job_number: 9882
exec_file: job_scripts/9882
submission_time: Sun Nov 13 20:18:34 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/chipseq.bds.20161113_130759_255_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_18.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/chipseq.bds.20161113_130759_255_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_18.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/4,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=8907.SRR1370888_1.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6,SSH_CONNECTION=171.65.77.8 55144 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file: STDIN
usage 1: cpu=00:02:03, mem=3.82195 GBs, io=1.60248, vmem=60.152M, maxvmem=298.840M
scheduling info: queue instance "amd.q@wotan" dropped because it is full
queue instance "q@kali" dropped because it is full
queue instance "q@surya" dropped because it is full
queue instance "q@nandi" dropped because it is full
queue instance "q@kadru" dropped because it is full
All queues dropped because of overload or full
|
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| string | _LMFILES_ | /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6 |
| bool | allowEmpty | false |
| string[] | args | [-title, SRR1370888_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370888_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| string | ASCPKEY | /software/ascp/etc/asperaweb_id_dsa.openssh |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DERBY_HOME | /usr/lib/jvm/java-8-oracle/db |
| string | DISPLAY | localhost:12.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| string | J2REDIR | /usr/lib/jvm/java-8-oracle/jre |
| string | J2SDKDIR | /usr/lib/jvm/java-8-oracle |
| string | JAVA_HOME | /usr/lib/jvm/java-8-oracle |
| int | K | 1024 |
| string | KERAS_DIR | /users/imk1/.local/lib/python2.7/site-packages/keras/ |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_N5SeQf |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6 |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESAPPSDIR | /software |
| string | MODULESHOME | /software/env_module/3.2.10 |
| string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect |
| string | PERL5LIB | /users/imk1/perl5/lib/perl5 |
| string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5 |
| string | PERL_MB_OPT | --install_base \"/users/imk1/perl5\" |
| string | PERL_MM_OPT | INSTALL_BASE=/users/imk1/perl5 |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1 |
| string | programName | chipseq.bds |
| string | programPath | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
| string | PWD | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1 |
| string | PYTHONPATH | /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/ |
| string | queue | |
| int | retry | 0 |
| string | RULEFITBASE | /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/ |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_CLIENT | 171.65.77.8 55144 22 |
| string | SSH_CONNECTION | 171.65.77.8 55144 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/4 |
| string | STY | 8907.SRR1370888_1.BDS |
| string | system | sge |
| int | T | 1099511627776 |
| string | TERM | screen |
| string | TERMCAP | SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD: |
| int | timeout | -1 |
| string | USER | imk1 |
| string | UTIL_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/ |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WINDOW | 0 |
| string | XDG_RUNTIME_DIR | /run/user/1048 |
| string | XDG_SESSION_ID | 20 |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |