Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170128_230219_262
Start time	2017-01-28 23:02:19
Run time	02:25:45.435
Tasks executed	26
Tasks failed	0
Tasks failed names
Arguments*	[-title, H3K27ac, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016003.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz, -final_stage, idr, -histone, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170128_230219_262/task.callpeak_macs2.macs2_rep1.line_71.id_25 chipseq.bds.20170128_230219_262/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26 chipseq.bds.20170128_230219_262/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27 chipseq.bds.20170128_230219_262/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28 chipseq.bds.20170128_230219_262/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29 chipseq.bds.20170128_230219_262/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30 chipseq.bds.20170128_230219_262/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31 chipseq.bds.20170128_230219_262/task.report.peak2hammock.line_412.id_32 chipseq.bds.20170128_230219_262/task.report.peak2hammock.line_412.id_33 chipseq.bds.20170128_230219_262/task.graphviz.report.line_97.id_34 chipseq.bds.20170128_230219_262/task.report.pdf2png.line_379.id_39
thread_41	thread_Root	chipseq.bds.20170128_230219_262_parallel_41/task.align_bwa.bwa_aln_rep1.line_111.id_10 chipseq.bds.20170128_230219_262_parallel_41/task.align_bwa.bwa_sam_rep1.line_143.id_12 chipseq.bds.20170128_230219_262_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18 chipseq.bds.20170128_230219_262_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_19 chipseq.bds.20170128_230219_262_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20170128_230219_262_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_21 chipseq.bds.20170128_230219_262_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_22 chipseq.bds.20170128_230219_262_parallel_41/task.postalign_bed.spr_rep1.line_255.id_23 chipseq.bds.20170128_230219_262_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_24
thread_42	thread_Root	chipseq.bds.20170128_230219_262_parallel_42/task.align_bwa.bwa_aln_ctl1.line_111.id_11 chipseq.bds.20170128_230219_262_parallel_42/task.align_bwa.bwa_sam_ctl1.line_143.id_13 chipseq.bds.20170128_230219_262_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14 chipseq.bds.20170128_230219_262_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_15 chipseq.bds.20170128_230219_262_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16 chipseq.bds.20170128_230219_262_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_17

Task details

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	35890

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-28 23:02:21
End	2017-01-28 23:52:31
Elapsed	00:50:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016003.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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/SRR1016003.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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--------------------
56734 (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] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.56 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 5.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.96 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.35 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 4.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.91 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.26 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.75 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.66 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.28 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.20 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.63 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.25 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.52 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.75 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.28 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.94 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.73 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.50 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.21 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.26 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.61 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.48 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.48 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.39 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.85 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.39 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.45 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.12 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.23 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.80 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.22 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.43 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.47 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.70 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.85 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.66 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.32 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.72 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.44 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.07 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.63 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.08 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.20 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.05 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.70 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.71 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.13 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.29 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.68 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.84 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.46 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.97 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.14 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.69 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 4.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.95 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.75 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.73 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.01 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.88 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.70 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.72 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.91 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.51 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.88 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.12 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.89 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.46 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.53 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.22 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.72 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.93 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.06 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.46 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.08 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.82 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.63 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.47 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.17 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.93 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.07 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.83 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.49 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.99 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.79 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.61 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.01 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.38 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.01 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.58 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.43 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.76 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.19 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.45 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.11 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.82 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.95 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 5.63 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 32529095 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/SRR1016003.fastq.gz
[main] Real time: 2988.923 sec; CPU: 8420.608 sec

Num	2
ID	task.align_bwa.bwa_aln_ctl1.line_111.id_11
Name	bwa_aln ctl1
Thread	thread_42
PID	35891

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-28 23:02:21
End	2017-01-29 00:06:27
Elapsed	01:04:05
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/H3K27ac/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/H3K27ac/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--------------------
56725 (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... 86.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.88 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... 53.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.14 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.21 sec
[bwa_aln_core] write to the disk... 0.04 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: 3825.588 sec; CPU: 3819.884 sec

Num	3
ID	task.align_bwa.bwa_sam_rep1.line_143.id_12
Name	bwa_sam rep1
Thread	thread_41
PID	35927

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-28 23:52:32
End	2017-01-29 00:39:43
Elapsed	00:47:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016003.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016003.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.bam

# SYS command. line 152

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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--------------------
59175 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.17 sec
[bwa_aln_core] refine gapped alignments... 2.77 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.74 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.31 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 5.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.89 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.55 sec
[bwa_aln_core] refine gapped alignments... 1.31 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.35 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 4.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.78 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.63 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.43 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.21 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.58 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.66 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.02 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.93 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.43 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.55 sec
[bwa_aln_core] refine gapped alignments... 1.40 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.58 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.60 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.72 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.04 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.69 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.16 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.12 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.42 sec
[bwa_aln_core] refine gapped alignments... 1.08 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.86 sec
[bwa_aln_core] refine gapped alignments... 2.13 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.17 sec
[bwa_aln_core] refine gapped alignments... 1.27 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.10 sec
[bwa_aln_core] refine gapped alignments... 1.32 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.70 sec
[bwa_aln_core] refine gapped alignments... 1.43 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.62 sec
[bwa_aln_core] refine gapped alignments... 1.50 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.35 sec
[bwa_aln_core] refine gapped alignments... 1.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.03 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.40 sec
[bwa_aln_core] refine gapped alignments... 1.77 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.15 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.70 sec
[bwa_aln_core] refine gapped alignments... 1.98 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.09 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.07 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.98 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.03 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.88 sec
[bwa_aln_core] refine gapped alignments... 2.28 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.66 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.61 sec
[bwa_aln_core] refine gapped alignments... 2.25 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.65 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.82 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.71 sec
[bwa_aln_core] refine gapped alignments... 2.24 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.89 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.73 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.00 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.79 sec
[bwa_aln_core] refine gapped alignments... 1.90 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.97 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.03 sec
[bwa_aln_core] refine gapped alignments... 2.28 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.19 sec
[bwa_aln_core] refine gapped alignments... 2.28 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.50 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.67 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.45 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.17 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.19 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.63 sec
[bwa_aln_core] refine gapped alignments... 2.37 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.24 sec
[bwa_aln_core] refine gapped alignments... 2.24 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.48 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.35 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.33 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.44 sec
[bwa_aln_core] refine gapped alignments... 2.25 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.10 sec
[bwa_aln_core] refine gapped alignments... 2.24 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.97 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.73 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.33 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.95 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.55 sec
[bwa_aln_core] refine gapped alignments... 2.28 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.78 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.85 sec
[bwa_aln_core] refine gapped alignments... 2.28 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.06 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 4.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.41 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.53 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.65 sec
[bwa_aln_core] refine gapped alignments... 2.24 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.18 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.40 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.58 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.92 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.82 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.53 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.60 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.58 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.83 sec
[bwa_aln_core] refine gapped alignments... 2.74 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.26 sec
[bwa_aln_core] refine gapped alignments... 2.75 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.75 sec
[bwa_aln_core] refine gapped alignments... 2.67 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.16 sec
[bwa_aln_core] refine gapped alignments... 2.67 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.82 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.60 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.40 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.85 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.85 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.67 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.85 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.40 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.65 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.26 sec
[bwa_aln_core] refine gapped alignments... 2.53 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.60 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.38 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.86 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.80 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.01 sec
[bwa_aln_core] refine gapped alignments... 2.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.83 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.22 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.42 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.42 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.74 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.74 sec
[bwa_aln_core] refine gapped alignments... 2.17 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.41 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.00 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.07 sec
[bwa_aln_core] refine gapped alignments... 1.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.99 sec
[bwa_aln_core] refine gapped alignments... 1.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.74 sec
[bwa_aln_core] refine gapped alignments... 1.54 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.82 sec
[bwa_aln_core] refine gapped alignments... 1.58 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.97 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.69 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.73 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.70 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.89 sec
[bwa_aln_core] refine gapped alignments... 1.52 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.05 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.95 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.13 sec
[bwa_aln_core] refine gapped alignments... 1.57 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.94 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.07 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.99 sec
[bwa_aln_core] refine gapped alignments... 1.37 sec
[bwa_aln_core] print alignments... 0.07 sec
[bwa_aln_core] 32529095 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/H3K27ac/out/align/rep1/SRR1016003.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016003.fastq.gz
[main] Real time: 2502.690 sec; CPU: 2412.212 sec

Num	4
ID	task.align_bwa.bwa_sam_ctl1.line_143.id_13
Name	bwa_sam ctl1
Thread	thread_42
PID	35951

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2017-01-29 00:06:28
End	2017-01-29 00:18:34
Elapsed	00:12:06
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/H3K27ac/out/align/ctl1/ENCFF001HNC.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/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/H3K27ac/out/align/ctl1/ENCFF001HNC.bam

# SYS command. line 152

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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--------------------
19319 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.05 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.52 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.26 sec
[bwa_aln_core] refine gapped alignments... 0.49 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... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.55 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.39 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.11 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.48 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3145728 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... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.02 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.99 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.90 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.44 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 4456448 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... 0.60 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.99 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.69 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.45 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.76 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.91 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 7864320 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... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 8650752 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... 0.47 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.73 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 1.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.01 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 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] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11010048 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... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.79 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 12058624 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... 0.52 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.48 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... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.53 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.47 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... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.32 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.43 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/H3K27ac/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 451.158 sec; CPU: 396.992 sec

Num	5
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	35970

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 00:18:36
End	2017-01-29 00:22:10
Elapsed	00:03:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/align/ctl1/ENCFF001HNC.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/align/ctl1/ENCFF001HNC.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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--------------------
3156 (process ID) old priority 0, new priority 10

Num	6
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_15
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	35977

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2017-01-29 00:22:12
End	2017-01-29 00:25:07
Elapsed	00:02:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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--------------------
7153 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:22:22 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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
[Sun Jan 29 00:22:22 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-29 00:22:22	MarkDuplicates	Start of doWork freeMemory: 254879680; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:22:22	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:22:22	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2017-01-29 00:22:31	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr2:7,720,599
INFO	2017-01-29 00:22:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:22:36	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    5s.  Last read position: chr3:32,290,878
INFO	2017-01-29 00:22:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:22:41	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    4s.  Last read position: chr5:31,410,244
INFO	2017-01-29 00:22:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:22:45	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    4s.  Last read position: chr6:76,055,404
INFO	2017-01-29 00:22:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:22:53	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    7s.  Last read position: chr7:134,138,515
INFO	2017-01-29 00:22:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:22:56	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    3s.  Last read position: chr9:137,609,223
INFO	2017-01-29 00:22:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:23:02	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    6s.  Last read position: chr11:121,062,334
INFO	2017-01-29 00:23:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:23:05	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    2s.  Last read position: chr14:86,188,790
INFO	2017-01-29 00:23:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:23:11	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    6s.  Last read position: chr17:58,813,264
INFO	2017-01-29 00:23:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:23:16	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    5s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:23:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:23:19	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    2s.  Last read position: chrX:100,440,272
INFO	2017-01-29 00:23:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:23:21	MarkDuplicates	Read 11369002 records. 0 pairs never matched.
INFO	2017-01-29 00:23:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3616771784; totalMemory: 4767875072; maxMemory: 11453595648
INFO	2017-01-29 00:23:24	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:23:25	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:23:25	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:23:25	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:23:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1834320672; totalMemory: 4767875072; maxMemory: 11453595648
INFO	2017-01-29 00:23:26	MarkDuplicates	Marking 167589 records as duplicates.
INFO	2017-01-29 00:23:26	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:24:55	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:29s.  Time for last 10,000,000:   89s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:25:05	MarkDuplicates	Before output close freeMemory: 8193961008; totalMemory: 8273264640; maxMemory: 11453595648
INFO	2017-01-29 00:25:05	MarkDuplicates	After output close freeMemory: 8304060328; totalMemory: 8383365120; maxMemory: 11453595648
[Sun Jan 29 00:25:06 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.73 minutes.
Runtime.totalMemory()=8383365120

Num	7
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	35981

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 00:25:09
End	2017-01-29 00:28:25
Elapsed	00:03:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/align/ctl1/ENCFF001HNC.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/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--------------------
7349 (process ID) old priority 0, new priority 10

Num	8
ID	task.postalign_bam.bam_to_tag_ctl1.line_505.id_17
Name	bam_to_tag ctl1
Thread	thread_42
PID	35987

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 00:28:27
End	2017-01-29 00:29:37
Elapsed	00:01:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/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/H3K27ac/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--------------------
38412 (process ID) old priority 0, new priority 10

Waiting for 37 seconds.

Num	9
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
Name	dedup_bam_1 rep1
Thread	thread_41
PID	36000

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-29 00:39:45
End	2017-01-29 00:43:17
Elapsed	00:03:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.bam | \
			    	sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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--------------------
8091 (process ID) old priority 0, new priority 10

Num	10
ID	task.postalign_bam.markdup_bam_picard_rep1.line_348.id_19
Name	markdup_bam_picard rep1
Thread	thread_41
PID	36006

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2017-01-29 00:43:18
End	2017-01-29 00:48:25
Elapsed	00:05:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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--------------------
8452 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:43:37 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Jan 29 00:43:37 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-29 00:43:37	MarkDuplicates	Start of doWork freeMemory: 254879712; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:43:37	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:43:37	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-29 00:43:39	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1016003.7010824'.  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	2017-01-29 00:43:46	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr1:67,831,811
INFO	2017-01-29 00:43:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:43:51	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    4s.  Last read position: chr1:212,088,186
INFO	2017-01-29 00:43:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:43:56	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    4s.  Last read position: chr2:74,003,822
INFO	2017-01-29 00:43:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:43:59	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    2s.  Last read position: chr2:231,531,981
INFO	2017-01-29 00:43:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:02	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    2s.  Last read position: chr3:136,196,153
INFO	2017-01-29 00:44:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:07	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    5s.  Last read position: chr4:85,095,328
INFO	2017-01-29 00:44:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:10	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    3s.  Last read position: chr5:105,768,006
INFO	2017-01-29 00:44:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:17	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    6s.  Last read position: chr6:25,519,859
INFO	2017-01-29 00:44:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:20	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    3s.  Last read position: chr6:157,990,226
INFO	2017-01-29 00:44:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:27	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    7s.  Last read position: chr7:110,998,804
INFO	2017-01-29 00:44:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:33	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    5s.  Last read position: chr8:133,131,288
INFO	2017-01-29 00:44:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:35	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chr10:13,346,852
INFO	2017-01-29 00:44:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:40	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    4s.  Last read position: chr10:128,127,233
INFO	2017-01-29 00:44:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:42	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    2s.  Last read position: chr12:2,795,467
INFO	2017-01-29 00:44:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:54	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:   11s.  Last read position: chr12:132,175,726
INFO	2017-01-29 00:44:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:56	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    2s.  Last read position: chr14:69,398,068
INFO	2017-01-29 00:44:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:44:59	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    2s.  Last read position: chr15:98,072,464
INFO	2017-01-29 00:44:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:45:03	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    4s.  Last read position: chr17:17,782,998
INFO	2017-01-29 00:45:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:45:05	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    2s.  Last read position: chr18:3,447,582
INFO	2017-01-29 00:45:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:45:13	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    7s.  Last read position: chr19:50,555,868
INFO	2017-01-29 00:45:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:45:15	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    2s.  Last read position: chr22:33,535,915
INFO	2017-01-29 00:45:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:45:17	MarkDuplicates	Read 21920718 records. 0 pairs never matched.
INFO	2017-01-29 00:45:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4206139624; totalMemory: 6038749184; maxMemory: 11453595648
INFO	2017-01-29 00:45:22	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:45:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:45:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:45:24	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:45:42	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5747771616; totalMemory: 8687976448; maxMemory: 11453595648
INFO	2017-01-29 00:45:42	MarkDuplicates	Marking 4031361 records as duplicates.
INFO	2017-01-29 00:45:42	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:46:52	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:10s.  Time for last 10,000,000:   70s.  Last read position: chr7:110,998,804
INFO	2017-01-29 00:48:08	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:26s.  Time for last 10,000,000:   76s.  Last read position: chr19:50,555,868
INFO	2017-01-29 00:48:23	MarkDuplicates	Before output close freeMemory: 8678624296; totalMemory: 8758231040; maxMemory: 11453595648
INFO	2017-01-29 00:48:24	MarkDuplicates	After output close freeMemory: 8826955240; totalMemory: 8906604544; maxMemory: 11453595648
[Sun Jan 29 00:48:24 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.79 minutes.
Runtime.totalMemory()=8906604544

Num	11
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
Name	dedup_bam_2 rep1
Thread	thread_41
PID	36020

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-29 00:48:26
End	2017-01-29 00:53:12
Elapsed	00:04:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.bam

# SYS command. line 153

 sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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/H3K27ac/out/qc/rep1/SRR1016003.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--------------------
52721 (process ID) old priority 0, new priority 10

Num	12
ID	task.postalign_bam.bam_to_tag_rep1.line_505.id_21
Name	bam_to_tag rep1
Thread	thread_41
PID	36031

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 00:53:13
End	2017-01-29 00:54:37
Elapsed	00:01:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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--------------------
14914 (process ID) old priority 0, new priority 10

Waiting for 17 seconds.

Num	13
ID	task.postalign_bed.subsample_tag_rep1.line_45.id_22
Name	subsample_tag rep1
Thread	thread_41
PID	36032

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 00:54:38
End	2017-01-29 00:55:51
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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--------------------
19580 (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	36033

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 00:54:40
End	2017-01-29 00:55:51
Elapsed	00:01:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.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--------------------
19581 (process ID) old priority 0, new priority 10
Waiting for 23 seconds.

Num	15
ID	task.postalign_bed.xcor_rep1.line_212.id_24
Name	xcor rep1
Thread	thread_41
PID	36034

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-29 00:55:53
End	2017-01-29 01:03:32
Elapsed	00:07:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.nodup.15M.tagAlign.gz -p=3 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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--------------------
8920 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.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/H3K27ac/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/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.15M.tagAlign.gz 
opened /tmp/36034.1.q/RtmpoR29Rq/SRR1016003.nodup.15M.tagAlign231671671986
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2154922 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.449931773677325,0.44991346505112 
Top 3 estimates for fragment length 150,160 
Window half size 830 
Phantom peak location 55 
Phantom peak Correlation 0.4174489 
Normalized Strand cross-correlation coefficient (NSC) 2.087926 
Relative Strand cross-correlation Coefficient (RSC) 1.160841 
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	36043

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:03:33
End	2017-01-29 01:24:56
Elapsed	00:21:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/signal/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/signal/macs2/rep1/SRR1016003.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/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1 -o "SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/signal/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1 -o "SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/signal/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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--------------------
51548 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 01:03:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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 01:03:53: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:03:53: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:03:54:  1000000 
INFO  @ Sun, 29 Jan 2017 01:03:56:  2000000 
INFO  @ Sun, 29 Jan 2017 01:03:57:  3000000 
INFO  @ Sun, 29 Jan 2017 01:03:58:  4000000 
INFO  @ Sun, 29 Jan 2017 01:04:00:  5000000 
INFO  @ Sun, 29 Jan 2017 01:04:01:  6000000 
INFO  @ Sun, 29 Jan 2017 01:04:03:  7000000 
INFO  @ Sun, 29 Jan 2017 01:04:04:  8000000 
INFO  @ Sun, 29 Jan 2017 01:04:06:  9000000 
INFO  @ Sun, 29 Jan 2017 01:04:07:  10000000 
INFO  @ Sun, 29 Jan 2017 01:04:09:  11000000 
INFO  @ Sun, 29 Jan 2017 01:04:10:  12000000 
INFO  @ Sun, 29 Jan 2017 01:04:11:  13000000 
INFO  @ Sun, 29 Jan 2017 01:04:13:  14000000 
INFO  @ Sun, 29 Jan 2017 01:04:14:  15000000 
INFO  @ Sun, 29 Jan 2017 01:04:16:  16000000 
INFO  @ Sun, 29 Jan 2017 01:04:17:  17000000 
INFO  @ Sun, 29 Jan 2017 01:04:19: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:04:20:  1000000 
INFO  @ Sun, 29 Jan 2017 01:04:21:  2000000 
INFO  @ Sun, 29 Jan 2017 01:04:23:  3000000 
INFO  @ Sun, 29 Jan 2017 01:04:24:  4000000 
INFO  @ Sun, 29 Jan 2017 01:04:25:  5000000 
INFO  @ Sun, 29 Jan 2017 01:04:27:  6000000 
INFO  @ Sun, 29 Jan 2017 01:04:28:  7000000 
INFO  @ Sun, 29 Jan 2017 01:04:30:  8000000 
INFO  @ Sun, 29 Jan 2017 01:04:31:  9000000 
INFO  @ Sun, 29 Jan 2017 01:04:32:  10000000 
INFO  @ Sun, 29 Jan 2017 01:04:34:  11000000 
INFO  @ Sun, 29 Jan 2017 01:04:34: #1 tag size is determined as 48 bps 
INFO  @ Sun, 29 Jan 2017 01:04:34: #1 tag size = 48 
INFO  @ Sun, 29 Jan 2017 01:04:34: #1  total tags in treatment: 17889357 
INFO  @ Sun, 29 Jan 2017 01:04:34: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:04:34: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:04:34: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:04:34: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:04:34: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:04:34: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:04:34: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 01:04:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:05:31: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 01:05:31: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 01:05:31: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 01:05:31: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 01:05:31: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:07:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:07:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 01:07:37: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 01:07:37: Done! 
INFO  @ Sun, 29 Jan 2017 01:07:40: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/rep1/SRR1016003.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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 01:07:40: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:07:40: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:07:42:  1000000 
INFO  @ Sun, 29 Jan 2017 01:07:43:  2000000 
INFO  @ Sun, 29 Jan 2017 01:07:44:  3000000 
INFO  @ Sun, 29 Jan 2017 01:07:46:  4000000 
INFO  @ Sun, 29 Jan 2017 01:07:47:  5000000 
INFO  @ Sun, 29 Jan 2017 01:07:49:  6000000 
INFO  @ Sun, 29 Jan 2017 01:07:50:  7000000 
INFO  @ Sun, 29 Jan 2017 01:07:51:  8000000 
INFO  @ Sun, 29 Jan 2017 01:07:53:  9000000 
INFO  @ Sun, 29 Jan 2017 01:07:54:  10000000 
INFO  @ Sun, 29 Jan 2017 01:07:56:  11000000 
INFO  @ Sun, 29 Jan 2017 01:07:57:  12000000 
INFO  @ Sun, 29 Jan 2017 01:07:58:  13000000 
INFO  @ Sun, 29 Jan 2017 01:08:00:  14000000 
INFO  @ Sun, 29 Jan 2017 01:08:01:  15000000 
INFO  @ Sun, 29 Jan 2017 01:08:03:  16000000 
INFO  @ Sun, 29 Jan 2017 01:08:04:  17000000 
INFO  @ Sun, 29 Jan 2017 01:08:06: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:08:07:  1000000 
INFO  @ Sun, 29 Jan 2017 01:08:08:  2000000 
INFO  @ Sun, 29 Jan 2017 01:08:10:  3000000 
INFO  @ Sun, 29 Jan 2017 01:08:11:  4000000 
INFO  @ Sun, 29 Jan 2017 01:08:12:  5000000 
INFO  @ Sun, 29 Jan 2017 01:08:14:  6000000 
INFO  @ Sun, 29 Jan 2017 01:08:15:  7000000 
INFO  @ Sun, 29 Jan 2017 01:08:17:  8000000 
INFO  @ Sun, 29 Jan 2017 01:08:18:  9000000 
INFO  @ Sun, 29 Jan 2017 01:08:20:  10000000 
INFO  @ Sun, 29 Jan 2017 01:08:21:  11000000 
INFO  @ Sun, 29 Jan 2017 01:08:22: #1 tag size is determined as 48 bps 
INFO  @ Sun, 29 Jan 2017 01:08:22: #1 tag size = 48 
INFO  @ Sun, 29 Jan 2017 01:08:22: #1  total tags in treatment: 17889357 
INFO  @ Sun, 29 Jan 2017 01:08:22: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:08:22: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:08:22: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:08:22: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:08:22: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:08:22: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:08:22: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 01:08:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:09:10: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:10:02: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:10:03: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 01:10:03: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 01:10:03: Done! 
INFO  @ Sun, 29 Jan 2017 01:10:07: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:10:36: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:11:08: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 01:11:25: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 29 Jan 2017 01:13:33: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 01:14:50: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Sun, 29 Jan 2017 01:17:25: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:17:53: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:18:25: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 01:18:41: Values in your input bedGraph files will be multiplied by 11.201413 ... 
INFO  @ Sun, 29 Jan 2017 01:20:54: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Sun, 29 Jan 2017 01:21:10: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 01:22:14: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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	36044

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:03:34
End	2017-01-29 01:09:07
Elapsed	00:05:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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--------------------
51549 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 01:03:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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 01:03:53: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:03:53: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:03:54:  1000000 
INFO  @ Sun, 29 Jan 2017 01:03:56:  2000000 
INFO  @ Sun, 29 Jan 2017 01:03:58:  3000000 
INFO  @ Sun, 29 Jan 2017 01:03:59:  4000000 
INFO  @ Sun, 29 Jan 2017 01:04:01:  5000000 
INFO  @ Sun, 29 Jan 2017 01:04:02:  6000000 
INFO  @ Sun, 29 Jan 2017 01:04:04:  7000000 
INFO  @ Sun, 29 Jan 2017 01:04:06:  8000000 
INFO  @ Sun, 29 Jan 2017 01:04:08: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:04:09:  1000000 
INFO  @ Sun, 29 Jan 2017 01:04:11:  2000000 
INFO  @ Sun, 29 Jan 2017 01:04:12:  3000000 
INFO  @ Sun, 29 Jan 2017 01:04:13:  4000000 
INFO  @ Sun, 29 Jan 2017 01:04:15:  5000000 
INFO  @ Sun, 29 Jan 2017 01:04:16:  6000000 
INFO  @ Sun, 29 Jan 2017 01:04:18:  7000000 
INFO  @ Sun, 29 Jan 2017 01:04:19:  8000000 
INFO  @ Sun, 29 Jan 2017 01:04:20:  9000000 
INFO  @ Sun, 29 Jan 2017 01:04:22:  10000000 
INFO  @ Sun, 29 Jan 2017 01:04:23:  11000000 
INFO  @ Sun, 29 Jan 2017 01:04:24: #1 tag size is determined as 48 bps 
INFO  @ Sun, 29 Jan 2017 01:04:24: #1 tag size = 48 
INFO  @ Sun, 29 Jan 2017 01:04:24: #1  total tags in treatment: 8944679 
INFO  @ Sun, 29 Jan 2017 01:04:24: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:04:24: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:04:24: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:04:24: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:04:24: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:04:24: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:04:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 01:04:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:05:05: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 01:05:05: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 01:05:05: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 01:05:05: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 01:05:05: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:06:41: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:06:41: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 01:06:42: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 01:06:42: Done! 
INFO  @ Sun, 29 Jan 2017 01:06:44: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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 01:06:44: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:06:44: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:06:46:  1000000 
INFO  @ Sun, 29 Jan 2017 01:06:48:  2000000 
INFO  @ Sun, 29 Jan 2017 01:06:49:  3000000 
INFO  @ Sun, 29 Jan 2017 01:06:51:  4000000 
INFO  @ Sun, 29 Jan 2017 01:06:52:  5000000 
INFO  @ Sun, 29 Jan 2017 01:06:54:  6000000 
INFO  @ Sun, 29 Jan 2017 01:06:55:  7000000 
INFO  @ Sun, 29 Jan 2017 01:06:57:  8000000 
INFO  @ Sun, 29 Jan 2017 01:06:59: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:07:00:  1000000 
INFO  @ Sun, 29 Jan 2017 01:07:02:  2000000 
INFO  @ Sun, 29 Jan 2017 01:07:03:  3000000 
INFO  @ Sun, 29 Jan 2017 01:07:04:  4000000 
INFO  @ Sun, 29 Jan 2017 01:07:06:  5000000 
INFO  @ Sun, 29 Jan 2017 01:07:07:  6000000 
INFO  @ Sun, 29 Jan 2017 01:07:09:  7000000 
INFO  @ Sun, 29 Jan 2017 01:07:10:  8000000 
INFO  @ Sun, 29 Jan 2017 01:07:11:  9000000 
INFO  @ Sun, 29 Jan 2017 01:07:13:  10000000 
INFO  @ Sun, 29 Jan 2017 01:07:14:  11000000 
INFO  @ Sun, 29 Jan 2017 01:07:15: #1 tag size is determined as 48 bps 
INFO  @ Sun, 29 Jan 2017 01:07:15: #1 tag size = 48 
INFO  @ Sun, 29 Jan 2017 01:07:15: #1  total tags in treatment: 8944679 
INFO  @ Sun, 29 Jan 2017 01:07:15: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:07:15: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:07:15: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:07:15: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:07:15: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:07:15: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:07:15: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 01:07:15: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:07:59: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:08:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:08:56: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 01:08:58: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 01:09:00: Done!

Num	18
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27
Name	macs2 rep1-pr2
Thread	thread_Root
PID	36045

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:03:35
End	2017-01-29 01:09:15
Elapsed	00:05:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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--------------------
51550 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 01:03:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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 01:03:53: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:03:53: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:03:54:  1000000 
INFO  @ Sun, 29 Jan 2017 01:03:56:  2000000 
INFO  @ Sun, 29 Jan 2017 01:03:57:  3000000 
INFO  @ Sun, 29 Jan 2017 01:03:59:  4000000 
INFO  @ Sun, 29 Jan 2017 01:04:00:  5000000 
INFO  @ Sun, 29 Jan 2017 01:04:02:  6000000 
INFO  @ Sun, 29 Jan 2017 01:04:04:  7000000 
INFO  @ Sun, 29 Jan 2017 01:04:05:  8000000 
INFO  @ Sun, 29 Jan 2017 01:04:07: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:04:09:  1000000 
INFO  @ Sun, 29 Jan 2017 01:04:10:  2000000 
INFO  @ Sun, 29 Jan 2017 01:04:11:  3000000 
INFO  @ Sun, 29 Jan 2017 01:04:13:  4000000 
INFO  @ Sun, 29 Jan 2017 01:04:14:  5000000 
INFO  @ Sun, 29 Jan 2017 01:04:15:  6000000 
INFO  @ Sun, 29 Jan 2017 01:04:17:  7000000 
INFO  @ Sun, 29 Jan 2017 01:04:18:  8000000 
INFO  @ Sun, 29 Jan 2017 01:04:20:  9000000 
INFO  @ Sun, 29 Jan 2017 01:04:21:  10000000 
INFO  @ Sun, 29 Jan 2017 01:04:22:  11000000 
INFO  @ Sun, 29 Jan 2017 01:04:23: #1 tag size is determined as 49 bps 
INFO  @ Sun, 29 Jan 2017 01:04:23: #1 tag size = 49 
INFO  @ Sun, 29 Jan 2017 01:04:23: #1  total tags in treatment: 8944678 
INFO  @ Sun, 29 Jan 2017 01:04:23: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:04:23: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:04:23: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:04:23: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:04:23: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:04:23: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:04:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 01:04:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:05:13: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 01:05:13: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 01:05:13: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 01:05:13: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 01:05:13: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:06:51: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:06:52: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 01:06:52: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 01:06:52: Done! 
INFO  @ Sun, 29 Jan 2017 01:06:55: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/align/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/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 01:06:55: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:06:55: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:06:57:  1000000 
INFO  @ Sun, 29 Jan 2017 01:06:58:  2000000 
INFO  @ Sun, 29 Jan 2017 01:07:00:  3000000 
INFO  @ Sun, 29 Jan 2017 01:07:01:  4000000 
INFO  @ Sun, 29 Jan 2017 01:07:03:  5000000 
INFO  @ Sun, 29 Jan 2017 01:07:04:  6000000 
INFO  @ Sun, 29 Jan 2017 01:07:06:  7000000 
INFO  @ Sun, 29 Jan 2017 01:07:08:  8000000 
INFO  @ Sun, 29 Jan 2017 01:07:10: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:07:11:  1000000 
INFO  @ Sun, 29 Jan 2017 01:07:12:  2000000 
INFO  @ Sun, 29 Jan 2017 01:07:14:  3000000 
INFO  @ Sun, 29 Jan 2017 01:07:15:  4000000 
INFO  @ Sun, 29 Jan 2017 01:07:17:  5000000 
INFO  @ Sun, 29 Jan 2017 01:07:18:  6000000 
INFO  @ Sun, 29 Jan 2017 01:07:19:  7000000 
INFO  @ Sun, 29 Jan 2017 01:07:21:  8000000 
INFO  @ Sun, 29 Jan 2017 01:07:22:  9000000 
INFO  @ Sun, 29 Jan 2017 01:07:24:  10000000 
INFO  @ Sun, 29 Jan 2017 01:07:25:  11000000 
INFO  @ Sun, 29 Jan 2017 01:07:26: #1 tag size is determined as 49 bps 
INFO  @ Sun, 29 Jan 2017 01:07:26: #1 tag size = 49 
INFO  @ Sun, 29 Jan 2017 01:07:26: #1  total tags in treatment: 8944678 
INFO  @ Sun, 29 Jan 2017 01:07:26: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:07:26: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:07:26: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:07:26: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:07:26: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:07:26: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:07:26: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 01:07:26: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:08:06: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:09:01: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:09:04: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 01:09:06: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 01:09:07: Done!

Num	19
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28
Name	naive_overlap_thresh
Thread	thread_Root
PID	36062

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:24:58
End	2017-01-29 01:26:21
Elapsed	00:01:23
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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--------------------
15183 (process ID) old priority 0, new priority 10
Waiting for 58 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN538364.1	121395	122073	Peak_2314	1411	.	52.77480	141.15765	137.42122	451

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN538364.1	121395	122073	Peak_2314	1411	.	52.77480	141.15765	137.42122	451

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1	121392	122047	Peak_3738	1129	.	44.09034	112.99314	109.53490	509

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1	121392	122047	Peak_3738	1129	.	44.09034	112.99314	109.53490	509

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2	140099	140729	Peak_10779	492	.	22.61635	49.24942	46.49529	324

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2	140099	140729	Peak_10779	492	.	22.61635	49.24942	46.49529	324

Num	20
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29
Name	naive_overlap_thresh
Thread	thread_Root
PID	36063

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:24:59
End	2017-01-29 01:26:22
Elapsed	00:01:23
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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--------------------
15184 (process ID) old priority 0, new priority 10
Waiting for 54 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN538364.1	182058	182208	Peak_7595	888	.	182058	182208	0	2	1,1	0,149	37.40998	92.07151	88.81216

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN538364.1	182058	182208	Peak_7595	888	.	182058	182208	0	2	1,1	0,149	37.40998	92.07151	88.81216

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1	121390	122057	Peak_59111	291	.	121390	122057	0	3	1,654,1	0,2,666	13.41379	30.75668	29.12277

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1	121390	122057	Peak_59111	291	.	121390	122057	0	3	1,654,1	0,2,666	13.41379	30.75668	29.12277

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000205.2	140097	140794	Peak_45166	33	.	140097	140794	0	3	1,629,1	0,2,696	2.53059	4.03530	3.32097

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000205.2	140097	140794	Peak_45166	33	.	140097	140794	0	3	1,629,1	0,2,696	2.53059	4.03530	3.32097

Num	21
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30
Name	naive_overlap_thresh
Thread	thread_Root
PID	36064

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:25:00
End	2017-01-29 01:26:22
Elapsed	00:01:22
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016003.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/H3K27ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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--------------------
15182 (process ID) old priority 0, new priority 10
Waiting for 56 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN538364.1	182058	182208	Peak_7595	888	.	37.40998	92.07151	88.81216

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN538364.1	182058	182208	Peak_7595	888	.	37.40998	92.07151	88.81216

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1	121390	122057	Peak_59111	291	.	13.41379	30.75668	29.12277

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1	121390	122057	Peak_59111	291	.	13.41379	30.75668	29.12277

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000205.2	140097	140794	Peak_45166	33	.	2.53059	4.03530	3.32097

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000205.2	140097	140794	Peak_45166	33	.	2.53059	4.03530	3.32097

Num	22
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31
Name	blacklist_filter peak 1
Thread	thread_Root
PID	19628

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:26:24
End	2017-01-29 01:27:33
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.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/H3K27ac/out/peak/macs2/rep1/SRR1016003.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--------------------
19633 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KN538364.1	121394	122057	Peak_2981	1505	.	53.87943	150.51297	146.96088	460

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/rep1/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KN538364.1	121394	122057	Peak_2981	1505	.	53.87943	150.51297	146.96088	460

Num	23
ID	task.report.peak2hammock.line_412.id_32
Name	peak2hammock
Thread	thread_Root
PID	23997

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:27:34
End	2017-01-29 01:27:43
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
24003 (process ID) old priority 0, new priority 10

Num	24
ID	task.report.peak2hammock.line_412.id_33
Name	peak2hammock
Thread	thread_Root
PID	24695

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:27:44
End	2017-01-29 01:27:55
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.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/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/peak/macs2/overlap/SRR1016003.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
24699 (process ID) old priority 0, new priority 10

Num	25
ID	task.graphviz.report.line_97.id_34
Name	report
Thread	thread_Root
PID	25454

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:27:55
End	2017-01-29 01:28:04
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/H3K27ac/out/report/H3K27ac_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/report/H3K27ac_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/report/H3K27ac_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
25459 (process ID) old priority 0, new priority 10

Num	26
ID	task.report.pdf2png.line_379.id_39
Name	pdf2png
Thread	thread_Root
PID	25460

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-29 01:27:56
End	2017-01-29 01:28:04
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.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/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac/out/qc/rep1/SRR1016003.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
25469 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, H3K27ac, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016003.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz, -final_stage, idr, -histone, $]
bool	canFail	false
string	CPATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_mOv3iE
string	LANG	en_US.UTF-8
string	LIBRARY_PATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K27ac
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 32974 22
string	SSH_CONNECTION	171.65.77.8 32974 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	28768.H3K27ac.BDS
string	system	sge
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int	timeout	-1
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	45170
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope