Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
Num | 1 | ID | task.align_bwa.bwa_aln_rep1.line_111.id_10 | Name | bwa_aln rep1 | Thread | thread_41 | PID | 35880 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-28 22:56:50 | End | 2017-01-28 23:23:12 | Elapsed | 00:26:22 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015997.fastq.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.sai
| Dependencies | | |
# SYS command. line 113
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 116
bwa aln -q 5 -l 32 -k 2 -t 3 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015997.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.sai
# SYS command. line 118
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
10509 (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] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 2.2% 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] 9961472 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% 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] 15990784 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.64 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 13.03 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 37073950 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 3 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015997.fastq.gz
[main] Real time: 1565.061 sec; CPU: 4444.444 sec
|
Num | 2 | ID | task.align_bwa.bwa_aln_ctl1.line_111.id_11 | Name | bwa_aln ctl1 | Thread | thread_42 | PID | 35881 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-28 22:56:50 | End | 2017-01-28 23:31:22 | Elapsed | 00:34:32 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.sai
| Dependencies | | |
# SYS command. line 113
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 116
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/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.sai
# SYS command. line 118
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
10510 (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] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% 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] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% 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] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% 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] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.42 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% 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] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17560427 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/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 2055.096 sec; CPU: 2054.380 sec
|
Num | 3 | ID | task.align_bwa.bwa_sam_rep1.line_143.id_12 | Name | bwa_sam rep1 | Thread | thread_41 | PID | 35901 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-28 23:23:13 | End | 2017-01-28 23:50:18 | Elapsed | 00:27:05 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015997.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.sai
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.flagstat.qc
| Dependencies | | |
# SYS command. line 145
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
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015997.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.bam
# SYS command. line 152
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.flagstat.qc
# SYS command. line 154
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
42714 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.55 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.24 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.92 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.25 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.82 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.44 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.19 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.12 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.79 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.74 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.14 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.33 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.08 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.49 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.93 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.44 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.10 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.18 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.97 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.58 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.52 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.31 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.69 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.20 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.84 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.49 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.09 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.02 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.42 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.46 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.90 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.73 sec
[bwa_aln_core] refine gapped alignments... 1.19 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.28 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.05 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.93 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.67 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.79 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.64 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.04 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.36 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.16 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.82 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.52 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.36 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.30 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.98 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.61 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.97 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.62 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.93 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.67 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.87 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.95 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.14 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.68 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.51 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.43 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.98 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.89 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.71 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.03 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.91 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.53 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.85 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.24 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.31 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.65 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.53 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.04 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.59 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.96 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.85 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.30 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.32 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.22 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.31 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.75 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.15 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.87 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.68 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.14 sec
[bwa_aln_core] 37073950 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/Liu2013Data/H3ac/out/align/rep1/SRR1015997.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015997.fastq.gz
[main] Real time: 1421.662 sec; CPU: 1362.040 sec
|
Num | 4 | ID | task.align_bwa.bwa_sam_ctl1.line_143.id_13 | Name | bwa_sam ctl1 | Thread | thread_42 | PID | 35904 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2017-01-28 23:31:24 | End | 2017-01-28 23:48:25 | Elapsed | 00:17:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.sai
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.flagstat.qc
| Dependencies | | |
# SYS command. line 145
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
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.bam
# SYS command. line 152
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.flagstat.qc
# SYS command. line 154
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
12382 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.05 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.43 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.62 sec
[bwa_aln_core] refine gapped alignments... 1.72 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.98 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.63 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 4.64 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.62 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.63 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.75 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.34 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.75 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.11 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.73 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.10 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.62 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.66 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.96 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.36 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.12 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.05 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.09 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.95 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.13 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.15 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.98 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.10 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.90 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.08 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.20 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.81 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.45 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.81 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.39 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.96 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.68 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.46 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.49 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.63 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.69 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.26 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.53 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.50 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.84 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 17560427 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/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 757.272 sec; CPU: 703.500 sec
|
Num | 5 | ID | task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14 | Name | dedup_bam_1 ctl1 | Thread | thread_42 | PID | 35918 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-28 23:48:27 | End | 2017-01-28 23:51:50 | Elapsed | 00:03:22 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.filt.bam
| Dependencies | | |
# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.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--------------------
12617 (process ID) old priority 0, new priority 10
|
Num | 6 | ID | task.postalign_bam.dedup_bam_1_rep1.line_95.id_15 | Name | dedup_bam_1 rep1 | Thread | thread_41 | PID | 35922 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-28 23:50:20 | End | 2017-01-28 23:53:51 | Elapsed | 00:03:31 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.filt.bam
| Dependencies | | |
# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; 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 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.bam | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
19674 (process ID) old priority 0, new priority 10
|
Num | 7 | ID | task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_16 | Name | markdup_bam_picard ctl1 | Thread | thread_42 | PID | 35926 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2017-01-28 23:51:52 | End | 2017-01-28 23:56:51 | Elapsed | 00:04:59 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.filt.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.dup.qc
| Dependencies | | |
# 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/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.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--------------------
58985 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sat Jan 28 23:52:11 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.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
[Sat Jan 28 23:52:11 PST 2017] Executing as imk1@wotan on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2017-01-28 23:52:11 MarkDuplicates Start of doWork freeMemory: 254878160; totalMemory: 257425408; maxMemory: 11453595648
INFO 2017-01-28 23:52:11 MarkDuplicates Reading input file and constructing read end information.
INFO 2017-01-28 23:52:11 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
INFO 2017-01-28 23:52:21 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr2:7,720,599
INFO 2017-01-28 23:52:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:52:28 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 7s. Last read position: chr3:32,290,878
INFO 2017-01-28 23:52:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:52:34 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 5s. Last read position: chr5:31,410,244
INFO 2017-01-28 23:52:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:52:40 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 6s. Last read position: chr6:76,055,404
INFO 2017-01-28 23:52:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:52:48 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 7s. Last read position: chr7:134,138,515
INFO 2017-01-28 23:52:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:52:53 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 5s. Last read position: chr9:137,609,223
INFO 2017-01-28 23:52:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:52:59 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 5s. Last read position: chr11:121,062,334
INFO 2017-01-28 23:52:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:53:04 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 5s. Last read position: chr14:86,188,790
INFO 2017-01-28 23:53:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:53:13 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 8s. Last read position: chr17:58,813,264
INFO 2017-01-28 23:53:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:53:18 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 5s. Last read position: chr20:35,666,706
INFO 2017-01-28 23:53:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:53:24 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 5s. Last read position: chrX:100,440,272
INFO 2017-01-28 23:53:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:53:26 MarkDuplicates Read 11369002 records. 0 pairs never matched.
INFO 2017-01-28 23:53:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 2411623128; totalMemory: 3537371136; maxMemory: 11453595648
INFO 2017-01-28 23:53:30 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk.
INFO 2017-01-28 23:53:37 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2017-01-28 23:53:37 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2017-01-28 23:53:38 MarkDuplicates Sorting list of duplicate records.
INFO 2017-01-28 23:53:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 3494605176; totalMemory: 6403653632; maxMemory: 11453595648
INFO 2017-01-28 23:53:40 MarkDuplicates Marking 167589 records as duplicates.
INFO 2017-01-28 23:53:40 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2017-01-28 23:56:26 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:46s. Time for last 10,000,000: 166s. Last read position: chr20:35,666,706
INFO 2017-01-28 23:56:50 MarkDuplicates Before output close freeMemory: 6682966440; totalMemory: 6737625088; maxMemory: 11453595648
INFO 2017-01-28 23:56:50 MarkDuplicates After output close freeMemory: 6755841312; totalMemory: 6810501120; maxMemory: 11453595648
[Sat Jan 28 23:56:50 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.66 minutes.
Runtime.totalMemory()=6810501120
|
Num | 8 | ID | task.postalign_bam.markdup_bam_picard_rep1.line_348.id_17 | Name | markdup_bam_picard rep1 | Thread | thread_41 | PID | 35928 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2017-01-28 23:53:52 | End | 2017-01-28 23:59:17 | Elapsed | 00:05:24 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.filt.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.dup.qc
| Dependencies | | |
# 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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
32108 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sat Jan 28 23:54:06 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.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
[Sat Jan 28 23:54:06 PST 2017] 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 2017-01-28 23:54:06 MarkDuplicates Start of doWork freeMemory: 254879792; totalMemory: 257425408; maxMemory: 11453595648
INFO 2017-01-28 23:54:06 MarkDuplicates Reading input file and constructing read end information.
INFO 2017-01-28 23:54:06 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
WARNING 2017-01-28 23:54:06 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1015997.7860072'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2017-01-28 23:54:09 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:45,303,181
INFO 2017-01-28 23:54:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:11 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:150,363,786
INFO 2017-01-28 23:54:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:14 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:227,734,867
INFO 2017-01-28 23:54:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:17 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr2:65,431,910
INFO 2017-01-28 23:54:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:19 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr2:189,661,554
INFO 2017-01-28 23:54:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:21 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr3:48,440,370
INFO 2017-01-28 23:54:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:24 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr3:160,754,862
INFO 2017-01-28 23:54:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:26 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr4:75,759,272
INFO 2017-01-28 23:54:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:30 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: chr5:61,334,547
INFO 2017-01-28 23:54:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:32 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr5:170,792,651
INFO 2017-01-28 23:54:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:34 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr6:87,695,639
INFO 2017-01-28 23:54:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:36 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr7:753,441
INFO 2017-01-28 23:54:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:39 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr7:105,532,720
INFO 2017-01-28 23:54:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:41 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr8:95,953,206
INFO 2017-01-28 23:54:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:43 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr9:114,176,684
INFO 2017-01-28 23:54:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:46 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr10:67,855,215
INFO 2017-01-28 23:54:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:52 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 6s. Last read position: chr11:13,700,261
INFO 2017-01-28 23:54:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:54 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr11:123,061,884
INFO 2017-01-28 23:54:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:54:59 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 4s. Last read position: chr12:90,337,068
INFO 2017-01-28 23:54:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:02 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr13:75,231,915
INFO 2017-01-28 23:55:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:03 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr14:90,579,262
INFO 2017-01-28 23:55:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:06 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr15:88,662,632
INFO 2017-01-28 23:55:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:09 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: chr16:66,605,458
INFO 2017-01-28 23:55:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:11 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr17:42,554,511
INFO 2017-01-28 23:55:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:14 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr18:3,445,903
INFO 2017-01-28 23:55:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:18 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 4s. Last read position: chr19:19,138,312
INFO 2017-01-28 23:55:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:20 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr20:39,431,870
INFO 2017-01-28 23:55:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:23 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: chr22:29,638,674
INFO 2017-01-28 23:55:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:25 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chrX:100,376,958
INFO 2017-01-28 23:55:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-28 23:55:32 MarkDuplicates Read 29381182 records. 0 pairs never matched.
INFO 2017-01-28 23:55:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 3333422048; totalMemory: 5628231680; maxMemory: 11453595648
INFO 2017-01-28 23:55:38 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk.
INFO 2017-01-28 23:55:38 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2017-01-28 23:55:38 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2017-01-28 23:55:40 MarkDuplicates Sorting list of duplicate records.
INFO 2017-01-28 23:55:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 2703453000; totalMemory: 5628231680; maxMemory: 11453595648
INFO 2017-01-28 23:55:41 MarkDuplicates Marking 5539449 records as duplicates.
INFO 2017-01-28 23:55:41 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2017-01-28 23:56:57 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:15s. Time for last 10,000,000: 75s. Last read position: chr5:170,792,651
INFO 2017-01-28 23:58:09 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:02:27s. Time for last 10,000,000: 72s. Last read position: chr13:75,231,915
INFO 2017-01-28 23:59:16 MarkDuplicates Before output close freeMemory: 8788171488; totalMemory: 8854700032; maxMemory: 11453595648
INFO 2017-01-28 23:59:16 MarkDuplicates After output close freeMemory: 8445810264; totalMemory: 8512339968; maxMemory: 11453595648
[Sat Jan 28 23:59:16 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 5.18 minutes.
Runtime.totalMemory()=8512339968
|
Num | 9 | ID | task.postalign_bam.dedup_bam_2_ctl1.line_144.id_18 | Name | dedup_bam_2 ctl1 | Thread | thread_42 | PID | 35933 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-28 23:56:53 | End | 2017-01-28 23:59:56 | Elapsed | 00:03:03 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.dupmark.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.nodup.pbc.qc
| Dependencies | | |
# 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/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3ac/out/qc/ctl1/ENCFF001HNC.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--------------------
42217 (process ID) old priority 0, new priority 10
|
Num | 10 | ID | task.postalign_bam.dedup_bam_2_rep1.line_144.id_19 | Name | dedup_bam_2 rep1 | Thread | thread_41 | PID | 35936 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-28 23:59:18 | End | 2017-01-29 00:11:42 | Elapsed | 00:12:23 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.dupmark.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.pbc.qc
| Dependencies | | |
# 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/Liu2013Data/H3ac/out/align/rep1/SRR1015997.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.bam
# SYS command. line 153
sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.bam
# SYS command. line 155
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
59486 (process ID) old priority 0, new priority 10
|
Num | 11 | ID | task.postalign_bam.bam_to_tag_ctl1.line_505.id_20 | Name | bam_to_tag ctl1 | Thread | thread_42 | PID | 35938 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-28 23:59:57 | End | 2017-01-29 00:01:06 | Elapsed | 00:01:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Dependencies | | |
# 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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
52149 (process ID) old priority 0, new priority 10
Waiting for 35 seconds.
|
Num | 12 | ID | task.postalign_bam.bam_to_tag_rep1.line_505.id_21 | Name | bam_to_tag rep1 | Thread | thread_41 | PID | 35957 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:11:43 | End | 2017-01-29 00:13:07 | Elapsed | 00:01:23 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz
| Dependencies | | |
# SYS command. line 507
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
36889 (process ID) old priority 0, new priority 10
|
Num | 13 | ID | task.postalign_bed.subsample_tag_rep1.line_45.id_22 | Name | subsample_tag rep1 | Thread | thread_41 | PID | 35959 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:13:09 | End | 2017-01-29 00:14:22 | Elapsed | 00:01:13 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.15M.tagAlign.gz
| Dependencies | | |
# SYS command. line 47
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 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.15M.tagAlign.gz
# SYS command. line 53
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
6536 (process ID) old priority 0, new priority 10
Waiting for 26 seconds.
|
Num | 14 | ID | task.postalign_bed.spr_rep1.line_255.id_23 | Name | spr rep1 | Thread | thread_41 | PID | 35960 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:13:10 | End | 2017-01-29 00:14:22 | Elapsed | 00:01:12 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz
| Dependencies | | |
# SYS command. line 257
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 260
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz | wc -l )
# SYS command. line 261
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 265
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.01
# SYS command. line 273
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
40904 (process ID) old priority 0, new priority 10
Waiting for 9 seconds.
|
Num | 15 | ID | task.postalign_bed.xcor_rep1.line_212.id_24 | Name | xcor rep1 | Thread | thread_41 | PID | 35961 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-29 00:14:23 | End | 2017-01-29 00:22:45 | Elapsed | 00:08:22 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.15M.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.plot.pdf
| Dependencies | | |
# SYS command. line 214
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 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.15M.tagAlign.gz -p=3 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
44870 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 3
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.15M.tagAlign.gz
opened /tmp/35961.1.q/Rtmp6VNljL/SRR1015997.nodup.15M.tagAlignb0f56d5bcd69
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.197866
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.339062429071147
Top 3 estimates for fragment length 160
Window half size 860
Phantom peak location 55
Phantom peak Correlation 0.3238354
Normalized Strand cross-correlation coefficient (NSC) 1.713597
Relative Strand cross-correlation Coefficient (RSC) 1.120878
Phantom Peak Quality Tag 1
null device
1
--------------------Stderr--------------------
Loading required package: caTools
|
Num | 16 | ID | task.callpeak_macs2.macs2_rep1.line_71.id_25 | Name | macs2 rep1 | Thread | thread_Root | PID | 35978 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:22:47 | End | 2017-01-29 00:47:46 | Elapsed | 00:24:59 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/signal/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/signal/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
| Dependencies | | |
# SYS command. line 73
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 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1 -o "SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/signal/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1 -o "SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/signal/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
17891 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 00:23:08:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 00:23:08: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:23:08: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:23:09: 1000000
INFO @ Sun, 29 Jan 2017 00:23:11: 2000000
INFO @ Sun, 29 Jan 2017 00:23:12: 3000000
INFO @ Sun, 29 Jan 2017 00:23:14: 4000000
INFO @ Sun, 29 Jan 2017 00:23:15: 5000000
INFO @ Sun, 29 Jan 2017 00:23:17: 6000000
INFO @ Sun, 29 Jan 2017 00:23:18: 7000000
INFO @ Sun, 29 Jan 2017 00:23:19: 8000000
INFO @ Sun, 29 Jan 2017 00:23:21: 9000000
INFO @ Sun, 29 Jan 2017 00:23:22: 10000000
INFO @ Sun, 29 Jan 2017 00:23:24: 11000000
INFO @ Sun, 29 Jan 2017 00:23:25: 12000000
INFO @ Sun, 29 Jan 2017 00:23:27: 13000000
INFO @ Sun, 29 Jan 2017 00:23:28: 14000000
INFO @ Sun, 29 Jan 2017 00:23:30: 15000000
INFO @ Sun, 29 Jan 2017 00:23:31: 16000000
INFO @ Sun, 29 Jan 2017 00:23:33: 17000000
INFO @ Sun, 29 Jan 2017 00:23:34: 18000000
INFO @ Sun, 29 Jan 2017 00:23:36: 19000000
INFO @ Sun, 29 Jan 2017 00:23:37: 20000000
INFO @ Sun, 29 Jan 2017 00:23:39: 21000000
INFO @ Sun, 29 Jan 2017 00:23:40: 22000000
INFO @ Sun, 29 Jan 2017 00:23:41: 23000000
INFO @ Sun, 29 Jan 2017 00:23:43: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:23:44: 1000000
INFO @ Sun, 29 Jan 2017 00:23:46: 2000000
INFO @ Sun, 29 Jan 2017 00:23:47: 3000000
INFO @ Sun, 29 Jan 2017 00:23:49: 4000000
INFO @ Sun, 29 Jan 2017 00:23:50: 5000000
INFO @ Sun, 29 Jan 2017 00:23:51: 6000000
INFO @ Sun, 29 Jan 2017 00:23:53: 7000000
INFO @ Sun, 29 Jan 2017 00:23:54: 8000000
INFO @ Sun, 29 Jan 2017 00:23:56: 9000000
INFO @ Sun, 29 Jan 2017 00:23:57: 10000000
INFO @ Sun, 29 Jan 2017 00:23:59: 11000000
INFO @ Sun, 29 Jan 2017 00:23:59: #1 tag size is determined as 49 bps
INFO @ Sun, 29 Jan 2017 00:23:59: #1 tag size = 49
INFO @ Sun, 29 Jan 2017 00:23:59: #1 total tags in treatment: 23841733
INFO @ Sun, 29 Jan 2017 00:23:59: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:23:59: #1 finished!
INFO @ Sun, 29 Jan 2017 00:23:59: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:23:59: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:23:59: #2 Use 160 as fragment length
INFO @ Sun, 29 Jan 2017 00:23:59: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:23:59: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 00:23:59: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:24:57: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 00:24:57: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 00:24:57: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 00:24:57: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 00:24:57: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:27:24: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 00:27:24: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 00:27:25: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 00:27:25: Done!
INFO @ Sun, 29 Jan 2017 00:27:27:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/rep1/SRR1015997.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 00:27:27: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:27:27: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:27:28: 1000000
INFO @ Sun, 29 Jan 2017 00:27:30: 2000000
INFO @ Sun, 29 Jan 2017 00:27:31: 3000000
INFO @ Sun, 29 Jan 2017 00:27:33: 4000000
INFO @ Sun, 29 Jan 2017 00:27:34: 5000000
INFO @ Sun, 29 Jan 2017 00:27:36: 6000000
INFO @ Sun, 29 Jan 2017 00:27:37: 7000000
INFO @ Sun, 29 Jan 2017 00:27:39: 8000000
INFO @ Sun, 29 Jan 2017 00:27:40: 9000000
INFO @ Sun, 29 Jan 2017 00:27:42: 10000000
INFO @ Sun, 29 Jan 2017 00:27:43: 11000000
INFO @ Sun, 29 Jan 2017 00:27:44: 12000000
INFO @ Sun, 29 Jan 2017 00:27:46: 13000000
INFO @ Sun, 29 Jan 2017 00:27:47: 14000000
INFO @ Sun, 29 Jan 2017 00:27:49: 15000000
INFO @ Sun, 29 Jan 2017 00:27:50: 16000000
INFO @ Sun, 29 Jan 2017 00:27:52: 17000000
INFO @ Sun, 29 Jan 2017 00:27:53: 18000000
INFO @ Sun, 29 Jan 2017 00:27:55: 19000000
INFO @ Sun, 29 Jan 2017 00:27:56: 20000000
INFO @ Sun, 29 Jan 2017 00:27:58: 21000000
INFO @ Sun, 29 Jan 2017 00:27:59: 22000000
INFO @ Sun, 29 Jan 2017 00:28:01: 23000000
INFO @ Sun, 29 Jan 2017 00:28:02: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:28:04: 1000000
INFO @ Sun, 29 Jan 2017 00:28:05: 2000000
INFO @ Sun, 29 Jan 2017 00:28:06: 3000000
INFO @ Sun, 29 Jan 2017 00:28:08: 4000000
INFO @ Sun, 29 Jan 2017 00:28:09: 5000000
INFO @ Sun, 29 Jan 2017 00:28:11: 6000000
INFO @ Sun, 29 Jan 2017 00:28:12: 7000000
INFO @ Sun, 29 Jan 2017 00:28:14: 8000000
INFO @ Sun, 29 Jan 2017 00:28:15: 9000000
INFO @ Sun, 29 Jan 2017 00:28:17: 10000000
INFO @ Sun, 29 Jan 2017 00:28:18: 11000000
INFO @ Sun, 29 Jan 2017 00:28:19: #1 tag size is determined as 49 bps
INFO @ Sun, 29 Jan 2017 00:28:19: #1 tag size = 49
INFO @ Sun, 29 Jan 2017 00:28:19: #1 total tags in treatment: 23841733
INFO @ Sun, 29 Jan 2017 00:28:19: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:28:19: #1 finished!
INFO @ Sun, 29 Jan 2017 00:28:19: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:28:19: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:28:19: #2 Use 160 as fragment length
INFO @ Sun, 29 Jan 2017 00:28:19: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:28:19: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 00:28:19: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:29:12: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:30:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 00:30:06: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 00:30:06: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 00:30:06: Done!
INFO @ Sun, 29 Jan 2017 00:30:11: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 00:30:54: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 00:31:28: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 00:31:50: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 29 Jan 2017 00:34:22: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 00:36:07: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'!
INFO @ Sun, 29 Jan 2017 00:39:39: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 00:40:21: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 00:40:53: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 00:41:12: Values in your input bedGraph files will be multiplied by 11.201413 ...
INFO @ Sun, 29 Jan 2017 00:43:44: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Sun, 29 Jan 2017 00:44:03: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 00:45:08: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'!
|
Num | 17 | ID | task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26 | Name | macs2 rep1-pr1 | Thread | thread_Root | PID | 35979 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:22:49 | End | 2017-01-29 00:28:31 | Elapsed | 00:05:41 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
| Dependencies | | |
# SYS command. line 73
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 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
17892 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 00:23:08:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 00:23:08: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:23:08: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:23:09: 1000000
INFO @ Sun, 29 Jan 2017 00:23:11: 2000000
INFO @ Sun, 29 Jan 2017 00:23:13: 3000000
INFO @ Sun, 29 Jan 2017 00:23:14: 4000000
INFO @ Sun, 29 Jan 2017 00:23:16: 5000000
INFO @ Sun, 29 Jan 2017 00:23:17: 6000000
INFO @ Sun, 29 Jan 2017 00:23:19: 7000000
INFO @ Sun, 29 Jan 2017 00:23:20: 8000000
INFO @ Sun, 29 Jan 2017 00:23:22: 9000000
INFO @ Sun, 29 Jan 2017 00:23:24: 10000000
INFO @ Sun, 29 Jan 2017 00:23:25: 11000000
INFO @ Sun, 29 Jan 2017 00:23:27: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:23:29: 1000000
INFO @ Sun, 29 Jan 2017 00:23:30: 2000000
INFO @ Sun, 29 Jan 2017 00:23:31: 3000000
INFO @ Sun, 29 Jan 2017 00:23:33: 4000000
INFO @ Sun, 29 Jan 2017 00:23:34: 5000000
INFO @ Sun, 29 Jan 2017 00:23:36: 6000000
INFO @ Sun, 29 Jan 2017 00:23:37: 7000000
INFO @ Sun, 29 Jan 2017 00:23:39: 8000000
INFO @ Sun, 29 Jan 2017 00:23:41: 9000000
INFO @ Sun, 29 Jan 2017 00:23:43: 10000000
INFO @ Sun, 29 Jan 2017 00:23:44: 11000000
INFO @ Sun, 29 Jan 2017 00:23:45: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 00:23:45: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 00:23:45: #1 total tags in treatment: 11920867
INFO @ Sun, 29 Jan 2017 00:23:45: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:23:45: #1 finished!
INFO @ Sun, 29 Jan 2017 00:23:45: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:23:45: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:23:45: #2 Use 160 as fragment length
INFO @ Sun, 29 Jan 2017 00:23:45: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:23:45: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 00:23:45: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:24:32: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 00:24:32: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 00:24:32: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 00:24:32: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 00:24:32: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:26:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 00:26:21: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 00:26:21: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 00:26:22: Done!
INFO @ Sun, 29 Jan 2017 00:26:24:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 00:26:24: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:26:24: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:26:25: 1000000
INFO @ Sun, 29 Jan 2017 00:26:27: 2000000
INFO @ Sun, 29 Jan 2017 00:26:28: 3000000
INFO @ Sun, 29 Jan 2017 00:26:30: 4000000
INFO @ Sun, 29 Jan 2017 00:26:31: 5000000
INFO @ Sun, 29 Jan 2017 00:26:33: 6000000
INFO @ Sun, 29 Jan 2017 00:26:35: 7000000
INFO @ Sun, 29 Jan 2017 00:26:36: 8000000
INFO @ Sun, 29 Jan 2017 00:26:38: 9000000
INFO @ Sun, 29 Jan 2017 00:26:39: 10000000
INFO @ Sun, 29 Jan 2017 00:26:41: 11000000
INFO @ Sun, 29 Jan 2017 00:26:43: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:26:44: 1000000
INFO @ Sun, 29 Jan 2017 00:26:45: 2000000
INFO @ Sun, 29 Jan 2017 00:26:47: 3000000
INFO @ Sun, 29 Jan 2017 00:26:48: 4000000
INFO @ Sun, 29 Jan 2017 00:26:50: 5000000
INFO @ Sun, 29 Jan 2017 00:26:51: 6000000
INFO @ Sun, 29 Jan 2017 00:26:52: 7000000
INFO @ Sun, 29 Jan 2017 00:26:54: 8000000
INFO @ Sun, 29 Jan 2017 00:26:55: 9000000
INFO @ Sun, 29 Jan 2017 00:26:57: 10000000
INFO @ Sun, 29 Jan 2017 00:26:58: 11000000
INFO @ Sun, 29 Jan 2017 00:26:59: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 00:26:59: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 00:26:59: #1 total tags in treatment: 11920867
INFO @ Sun, 29 Jan 2017 00:26:59: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:26:59: #1 finished!
INFO @ Sun, 29 Jan 2017 00:26:59: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:26:59: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:26:59: #2 Use 160 as fragment length
INFO @ Sun, 29 Jan 2017 00:26:59: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:26:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 00:26:59: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:27:44: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:28:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 00:28:25: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 00:28:26: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 00:28:26: Done!
|
Num | 18 | ID | task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27 | Name | macs2 rep1-pr2 | Thread | thread_Root | PID | 35980 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:22:49 | End | 2017-01-29 00:28:40 | Elapsed | 00:05:50 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
| Dependencies | | |
# SYS command. line 73
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 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
17893 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 00:23:08:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 00:23:08: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:23:08: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:23:10: 1000000
INFO @ Sun, 29 Jan 2017 00:23:11: 2000000
INFO @ Sun, 29 Jan 2017 00:23:13: 3000000
INFO @ Sun, 29 Jan 2017 00:23:14: 4000000
INFO @ Sun, 29 Jan 2017 00:23:16: 5000000
INFO @ Sun, 29 Jan 2017 00:23:18: 6000000
INFO @ Sun, 29 Jan 2017 00:23:20: 7000000
INFO @ Sun, 29 Jan 2017 00:23:21: 8000000
INFO @ Sun, 29 Jan 2017 00:23:23: 9000000
INFO @ Sun, 29 Jan 2017 00:23:25: 10000000
INFO @ Sun, 29 Jan 2017 00:23:26: 11000000
INFO @ Sun, 29 Jan 2017 00:23:28: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:23:30: 1000000
INFO @ Sun, 29 Jan 2017 00:23:31: 2000000
INFO @ Sun, 29 Jan 2017 00:23:33: 3000000
INFO @ Sun, 29 Jan 2017 00:23:34: 4000000
INFO @ Sun, 29 Jan 2017 00:23:36: 5000000
INFO @ Sun, 29 Jan 2017 00:23:37: 6000000
INFO @ Sun, 29 Jan 2017 00:23:39: 7000000
INFO @ Sun, 29 Jan 2017 00:23:41: 8000000
INFO @ Sun, 29 Jan 2017 00:23:42: 9000000
INFO @ Sun, 29 Jan 2017 00:23:44: 10000000
INFO @ Sun, 29 Jan 2017 00:23:45: 11000000
INFO @ Sun, 29 Jan 2017 00:23:46: #1 tag size is determined as 48 bps
INFO @ Sun, 29 Jan 2017 00:23:46: #1 tag size = 48
INFO @ Sun, 29 Jan 2017 00:23:46: #1 total tags in treatment: 11920866
INFO @ Sun, 29 Jan 2017 00:23:46: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:23:46: #1 finished!
INFO @ Sun, 29 Jan 2017 00:23:46: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:23:46: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:23:46: #2 Use 160 as fragment length
INFO @ Sun, 29 Jan 2017 00:23:46: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:23:46: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 00:23:46: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:24:33: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 00:24:33: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 00:24:33: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 00:24:33: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 00:24:33: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:26:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 00:26:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 00:26:25: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 00:26:25: Done!
INFO @ Sun, 29 Jan 2017 00:26:27:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 00:26:27: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:26:27: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:26:29: 1000000
INFO @ Sun, 29 Jan 2017 00:26:31: 2000000
INFO @ Sun, 29 Jan 2017 00:26:32: 3000000
INFO @ Sun, 29 Jan 2017 00:26:34: 4000000
INFO @ Sun, 29 Jan 2017 00:26:35: 5000000
INFO @ Sun, 29 Jan 2017 00:26:37: 6000000
INFO @ Sun, 29 Jan 2017 00:26:38: 7000000
INFO @ Sun, 29 Jan 2017 00:26:40: 8000000
INFO @ Sun, 29 Jan 2017 00:26:41: 9000000
INFO @ Sun, 29 Jan 2017 00:26:43: 10000000
INFO @ Sun, 29 Jan 2017 00:26:44: 11000000
INFO @ Sun, 29 Jan 2017 00:26:47: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:26:48: 1000000
INFO @ Sun, 29 Jan 2017 00:26:49: 2000000
INFO @ Sun, 29 Jan 2017 00:26:51: 3000000
INFO @ Sun, 29 Jan 2017 00:26:52: 4000000
INFO @ Sun, 29 Jan 2017 00:26:53: 5000000
INFO @ Sun, 29 Jan 2017 00:26:55: 6000000
INFO @ Sun, 29 Jan 2017 00:26:56: 7000000
INFO @ Sun, 29 Jan 2017 00:26:58: 8000000
INFO @ Sun, 29 Jan 2017 00:26:59: 9000000
INFO @ Sun, 29 Jan 2017 00:27:00: 10000000
INFO @ Sun, 29 Jan 2017 00:27:02: 11000000
INFO @ Sun, 29 Jan 2017 00:27:02: #1 tag size is determined as 48 bps
INFO @ Sun, 29 Jan 2017 00:27:02: #1 tag size = 48
INFO @ Sun, 29 Jan 2017 00:27:02: #1 total tags in treatment: 11920866
INFO @ Sun, 29 Jan 2017 00:27:02: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:27:02: #1 finished!
INFO @ Sun, 29 Jan 2017 00:27:02: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:27:02: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:27:02: #2 Use 160 as fragment length
INFO @ Sun, 29 Jan 2017 00:27:02: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:27:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 00:27:02: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:27:49: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:28:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 00:28:35: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 00:28:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 00:28:36: Done!
|
Num | 19 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 36015 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:47:48 | End | 2017-01-29 00:49:07 | Elapsed | 00:01:18 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 61
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 64
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | \
intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz
# SYS command. line 72
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
# SYS command. line 74
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz
# SYS command. line 76
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
50541 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1 15425 17220 Peak_1598 1292 . 47.47647 129.22035 125.13374 1032
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1 15425 17220 Peak_1598 1292 . 47.47647 129.22035 125.13374 1032
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1 15449 17420 Peak_2410 1168 . 43.52312 116.88520 113.02871 946
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1 15449 17420 Peak_2410 1168 . 43.52312 116.88520 113.02871 946
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1 68186 68965 Peak_18920 75 . 4.87496 7.53305 5.26948 488
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1 68186 68965 Peak_18920 75 . 4.87496 7.53305 5.26948 488
|
Num | 20 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 36016 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:47:50 | End | 2017-01-29 00:49:07 | Elapsed | 00:01:17 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
| Dependencies | | |
# SYS command. line 61
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 64
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | \
intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz
# SYS command. line 72
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
# SYS command. line 74
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz
# SYS command. line 76
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
50538 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1 14320 17465 Peak_29021 193 . 14320 17465 0 3 1,1795,1 0,1105,3144 8.63152 20.78147 19.36516
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1 14320 17465 Peak_29021 193 . 14320 17465 0 3 1,1795,1 0,1105,3144 8.63152 20.78147 19.36516
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1 18322 18663 Peak_19765 275 . 18322 18663 0 2 1,1 0,340 11.43586 28.82963 27.57722
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1 18322 18663 Peak_19765 275 . 18322 18663 0 2 1,1 0,340 11.43586 28.82963 27.57722
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1 66994 67154 Peak_79556 0 . 66994 67154 0 2 1,1 0,159 1.57091 1.12484 0.05306
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1 66994 67154 Peak_79556 0 . 66994 67154 0 2 1,1 0,159 1.57091 1.12484 0.05306
|
Num | 21 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 36017 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:47:51 | End | 2017-01-29 00:49:06 | Elapsed | 00:01:15 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
| Dependencies | | |
# SYS command. line 61
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 64
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015997.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | \
intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015997.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz
# SYS command. line 72
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
# SYS command. line 74
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz
# SYS command. line 76
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
50539 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1 14320 17465 Peak_29021 193 . 8.63152 20.78147 19.36516
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1 14320 17465 Peak_29021 193 . 8.63152 20.78147 19.36516
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1 18322 18663 Peak_19765 275 . 11.43586 28.82963 27.57722
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1 18322 18663 Peak_19765 275 . 11.43586 28.82963 27.57722
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1 66994 67154 Peak_79556 0 . 1.57091 1.12484 0.05306
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1 66994 67154 Peak_79556 0 . 1.57091 1.12484 0.05306
|
Num | 22 | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31 | Name | blacklist_filter peak 1 | Thread | thread_Root | PID | 55517 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:49:09 | End | 2017-01-29 00:50:17 | Elapsed | 00:01:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 29
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 31
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
55521 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KI270830.1 15425 17420 Peak_1851 1189 . 44.37027 118.92655 114.99937 971
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/rep1/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KI270830.1 15425 17420 Peak_1851 1189 . 44.37027 118.92655 114.99937 971
|
Num | 23 | ID | task.report.peak2hammock.line_412.id_32 | Name | peak2hammock | Thread | thread_Root | PID | 2960 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:50:18 | End | 2017-01-29 00:50:27 | Elapsed | 00:00:09 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
| Dependencies | | |
# SYS command. line 414
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 415
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
# SYS command. line 417
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock
# SYS command. line 418
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
--------------------Stdout--------------------
2964 (process ID) old priority 0, new priority 10
|
Num | 24 | ID | task.report.peak2hammock.line_412.id_33 | Name | peak2hammock | Thread | thread_Root | PID | 3624 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:50:28 | End | 2017-01-29 00:50:38 | Elapsed | 00:00:10 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock.gz
| Dependencies | | |
# SYS command. line 414
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 415
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
# SYS command. line 417
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock
# SYS command. line 418
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/peak/macs2/overlap/SRR1015997.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
--------------------Stdout--------------------
3628 (process ID) old priority 0, new priority 10
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Num | 25 | ID | task.graphviz.report.line_97.id_34 | Name | report | Thread | thread_Root | PID | 4303 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:50:39 | End | 2017-01-29 00:50:47 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | | Output files | | Dependencies | | |
# SYS command. line 98
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 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/report/H3ac_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/report/H3ac_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/report/H3ac_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout--------------------
4309 (process ID) old priority 0, new priority 10
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Num | 26 | ID | task.report.pdf2png.line_379.id_39 | Name | pdf2png | Thread | thread_Root | PID | 4308 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:50:39 | End | 2017-01-29 00:50:47 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.plot.pdf
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.plot.png
| Dependencies | | |
# SYS command. line 380
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 381
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3ac/out/qc/rep1/SRR1015997.nodup.15M.cc.plot.pdf
--------------------Stdout--------------------
4316 (process ID) old priority 0, new priority 10
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