Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170128_230109_051
Start time	2017-01-28 23:01:09
Run time	02:19:48.571
Tasks executed	26
Tasks failed	0
Tasks failed names
Arguments*	[-title, H3K4me1, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016001.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_230109_051/task.callpeak_macs2.macs2_rep1.line_71.id_25 chipseq.bds.20170128_230109_051/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26 chipseq.bds.20170128_230109_051/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27 chipseq.bds.20170128_230109_051/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28 chipseq.bds.20170128_230109_051/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29 chipseq.bds.20170128_230109_051/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30 chipseq.bds.20170128_230109_051/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31 chipseq.bds.20170128_230109_051/task.report.peak2hammock.line_412.id_32 chipseq.bds.20170128_230109_051/task.report.peak2hammock.line_412.id_33 chipseq.bds.20170128_230109_051/task.graphviz.report.line_97.id_34 chipseq.bds.20170128_230109_051/task.report.pdf2png.line_379.id_39
thread_41	thread_Root	chipseq.bds.20170128_230109_051_parallel_41/task.align_bwa.bwa_aln_rep1.line_111.id_10 chipseq.bds.20170128_230109_051_parallel_41/task.align_bwa.bwa_sam_rep1.line_143.id_12 chipseq.bds.20170128_230109_051_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18 chipseq.bds.20170128_230109_051_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_19 chipseq.bds.20170128_230109_051_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20170128_230109_051_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_21 chipseq.bds.20170128_230109_051_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_22 chipseq.bds.20170128_230109_051_parallel_41/task.postalign_bed.spr_rep1.line_255.id_23 chipseq.bds.20170128_230109_051_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_24
thread_42	thread_Root	chipseq.bds.20170128_230109_051_parallel_42/task.align_bwa.bwa_aln_ctl1.line_111.id_11 chipseq.bds.20170128_230109_051_parallel_42/task.align_bwa.bwa_sam_ctl1.line_143.id_13 chipseq.bds.20170128_230109_051_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14 chipseq.bds.20170128_230109_051_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_15 chipseq.bds.20170128_230109_051_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16 chipseq.bds.20170128_230109_051_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	35888

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

Start	2017-01-28 23:01:10
End	2017-01-28 23:48:16
Elapsed	00:47:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016001.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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/SRR1016001.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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--------------------
56568 (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] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.76 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.02 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.11 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.12 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.87 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.01 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.74 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.41 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.87 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.81 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.88 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.08 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.11 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.64 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.00 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.43 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.33 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.27 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.13 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.06 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.19 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.42 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.95 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.33 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.03 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.95 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.37 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.16 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.12 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.15 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.60 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.00 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.17 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.13 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.46 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.78 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.43 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.16 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.03 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.96 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.45 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.20 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.04 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.59 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.32 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.33 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.70 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.24 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.66 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.25 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.74 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.20 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.53 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.20 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.71 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.21 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.18 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.44 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.75 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.37 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.28 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.10 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.09 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.36 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.60 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.86 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.95 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.81 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.74 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.88 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.38 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.25 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.80 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.31 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.66 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.86 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.73 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.63 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.41 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.90 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.49 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.03 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.72 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.75 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.80 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.77 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.40 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.25 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.32 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.28 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.68 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.53 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.67 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.61 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26140017 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/SRR1016001.fastq.gz
[main] Real time: 2811.119 sec; CPU: 8083.668 sec

Num	2
ID	task.align_bwa.bwa_aln_ctl1.line_111.id_11
Name	bwa_aln ctl1
Thread	thread_42
PID	35889

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

Start	2017-01-28 23:01:10
End	2017-01-29 00:00:05
Elapsed	00:58:54
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/H3K4me1/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/H3K4me1/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--------------------
56567 (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... 51.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.69 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... 61.32 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... 76.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.46 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... 63.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.95 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... 50.15 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... 54.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.13 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... 53.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.33 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... 49.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.02 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... 48.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.07 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... 48.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.79 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... 49.43 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... 49.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.47 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... 49.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.44 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... 49.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.15 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... 49.43 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... 49.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.80 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... 49.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.27 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... 49.43 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... 49.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.05 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... 50.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.61 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... 57.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16252928 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... 0.07 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.71 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... 48.77 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... 48.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.05 sec
[bwa_aln_core] write to the disk... 0.06 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: 3520.022 sec; CPU: 3514.372 sec

Num	3
ID	task.align_bwa.bwa_sam_rep1.line_143.id_12
Name	bwa_sam rep1
Thread	thread_41
PID	35917

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

Start	2017-01-28 23:48:17
End	2017-01-29 00:29:16
Elapsed	00:40:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016001.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016001.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.bam

# SYS command. line 152

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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--------------------
58697 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.35 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.88 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.26 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.40 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.55 sec
[bwa_aln_core] refine gapped alignments... 2.24 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.14 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.17 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.58 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.24 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.28 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.57 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.64 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.28 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.41 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.34 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.41 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.52 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.69 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.29 sec
[bwa_aln_core] refine gapped alignments... 1.59 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.76 sec
[bwa_aln_core] refine gapped alignments... 1.33 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.85 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.27 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.59 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.31 sec
[bwa_aln_core] refine gapped alignments... 2.60 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.79 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.75 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.94 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.99 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.72 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.87 sec
[bwa_aln_core] refine gapped alignments... 2.53 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.16 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.54 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.45 sec
[bwa_aln_core] refine gapped alignments... 2.49 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.42 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.40 sec
[bwa_aln_core] refine gapped alignments... 2.41 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.63 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.81 sec
[bwa_aln_core] refine gapped alignments... 1.14 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.53 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.25 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.54 sec
[bwa_aln_core] refine gapped alignments... 2.72 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.38 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.76 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.98 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.27 sec
[bwa_aln_core] refine gapped alignments... 2.72 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.92 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.81 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.26 sec
[bwa_aln_core] refine gapped alignments... 2.58 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.80 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.43 sec
[bwa_aln_core] refine gapped alignments... 2.67 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.98 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.45 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.71 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.93 sec
[bwa_aln_core] refine gapped alignments... 2.60 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.77 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.29 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.37 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.55 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.59 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.65 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.94 sec
[bwa_aln_core] refine gapped alignments... 2.52 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.65 sec
[bwa_aln_core] refine gapped alignments... 2.67 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.08 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.67 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.62 sec
[bwa_aln_core] refine gapped alignments... 2.80 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.24 sec
[bwa_aln_core] refine gapped alignments... 2.52 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.39 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.67 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.23 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.13 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.57 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.42 sec
[bwa_aln_core] refine gapped alignments... 2.67 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.92 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.08 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.02 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.89 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.72 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.97 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.41 sec
[bwa_aln_core] refine gapped alignments... 2.53 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.40 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.18 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.65 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.41 sec
[bwa_aln_core] refine gapped alignments... 1.99 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.90 sec
[bwa_aln_core] refine gapped alignments... 2.52 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.07 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.61 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.22 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.27 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.33 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.48 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.48 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.73 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.38 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.75 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.09 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.12 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.07 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.84 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.33 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.91 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.89 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.55 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 26140017 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/H3K4me1/out/align/rep1/SRR1016001.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016001.fastq.gz
[main] Real time: 2172.693 sec; CPU: 2098.796 sec

Num	4
ID	task.align_bwa.bwa_sam_ctl1.line_143.id_13
Name	bwa_sam ctl1
Thread	thread_42
PID	35939

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

Start	2017-01-29 00:00:06
End	2017-01-29 00:11:42
Elapsed	00:11:35
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/H3K4me1/out/align/ctl1/ENCFF001HNC.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/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/H3K4me1/out/align/ctl1/ENCFF001HNC.bam

# SYS command. line 152

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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--------------------
53162 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.49 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.51 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... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 1310720 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... 0.31 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.62 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 2.03 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.28 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 3670016 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... 0.49 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.02 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 4718592 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... 0.44 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.00 sec
[bwa_aln_core] refine gapped alignments... 1.14 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 6553600 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... 0.48 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 7077888 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... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.18 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.50 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8912896 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... 0.58 sec
[bwa_aln_core] 9175040 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... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9437184 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... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 9699328 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... 0.48 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.29 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 10485760 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... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.32 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.02 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.64 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 14942208 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... 0.33 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.30 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.48 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.44 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.10 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.31 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/H3K4me1/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 428.487 sec; CPU: 375.128 sec

Num	5
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	35956

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

Start	2017-01-29 00:11:43
End	2017-01-29 00:15:20
Elapsed	00:03:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/align/ctl1/ENCFF001HNC.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/align/ctl1/ENCFF001HNC.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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--------------------
36890 (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	35963

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

Start	2017-01-29 00:15:21
End	2017-01-29 00:18:28
Elapsed	00:03:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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--------------------
48256 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:15:36 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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 00:15:36 PST 2017] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-29 00:15:36	MarkDuplicates	Start of doWork freeMemory: 254879688; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:15:36	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:15:36	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2017-01-29 00:15:46	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr2:7,720,599
INFO	2017-01-29 00:15:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:15:55	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    9s.  Last read position: chr3:32,290,878
INFO	2017-01-29 00:15:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:03	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    7s.  Last read position: chr5:31,410,244
INFO	2017-01-29 00:16:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:07	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    3s.  Last read position: chr6:76,055,404
INFO	2017-01-29 00:16:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:10	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    3s.  Last read position: chr7:134,138,515
INFO	2017-01-29 00:16:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:13	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    3s.  Last read position: chr9:137,609,223
INFO	2017-01-29 00:16:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:16	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    2s.  Last read position: chr11:121,062,334
INFO	2017-01-29 00:16:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:21	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    5s.  Last read position: chr14:86,188,790
INFO	2017-01-29 00:16:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:29	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    7s.  Last read position: chr17:58,813,264
INFO	2017-01-29 00:16:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:31	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    2s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:16:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:35	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    3s.  Last read position: chrX:100,440,272
INFO	2017-01-29 00:16:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:36	MarkDuplicates	Read 11369002 records. 0 pairs never matched.
INFO	2017-01-29 00:16:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3364505728; totalMemory: 4511498240; maxMemory: 11453595648
INFO	2017-01-29 00:16:39	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:16:42	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:16:42	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:16:42	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:16:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1581816856; totalMemory: 4511498240; maxMemory: 11453595648
INFO	2017-01-29 00:16:44	MarkDuplicates	Marking 167589 records as duplicates.
INFO	2017-01-29 00:16:44	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:18:17	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:33s.  Time for last 10,000,000:   93s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:18:27	MarkDuplicates	Before output close freeMemory: 8023797296; totalMemory: 8103395328; maxMemory: 11453595648
INFO	2017-01-29 00:18:27	MarkDuplicates	After output close freeMemory: 8129178024; totalMemory: 8208777216; maxMemory: 11453595648
[Sun Jan 29 00:18:27 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.85 minutes.
Runtime.totalMemory()=8208777216

Num	7
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	35969

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

Start	2017-01-29 00:18:30
End	2017-01-29 00:21:38
Elapsed	00:03:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/align/ctl1/ENCFF001HNC.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/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--------------------
3155 (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	35975

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

Start	2017-01-29 00:21:40
End	2017-01-29 00:22:51
Elapsed	00:01:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/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/H3K4me1/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--------------------
13392 (process ID) old priority 0, new priority 10

Waiting for 35 seconds.

Num	9
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
Name	dedup_bam_1 rep1
Thread	thread_41
PID	35988

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

Start	2017-01-29 00:29:18
End	2017-01-29 00:32:02
Elapsed	00:02:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.bam | \
			    	sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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--------------------
41746 (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	35990

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

Start	2017-01-29 00:32:04
End	2017-01-29 00:37:06
Elapsed	00:05:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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--------------------
7764 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:32:22 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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 00:32:22 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 00:32:22	MarkDuplicates	Start of doWork freeMemory: 254879568; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:32:22	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:32:22	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-29 00:32:24	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1016001.11584053'.  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 00:32:31	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr1:101,942,776
INFO	2017-01-29 00:32:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:32:39	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    7s.  Last read position: chr1:237,432,745
INFO	2017-01-29 00:32:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:32:43	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    4s.  Last read position: chr2:134,920,628
INFO	2017-01-29 00:32:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:32:48	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    5s.  Last read position: chr3:36,736,036
INFO	2017-01-29 00:32:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:32:56	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    7s.  Last read position: chr3:182,058,384
INFO	2017-01-29 00:32:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:32:59	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    3s.  Last read position: chr4:135,961,719
INFO	2017-01-29 00:32:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:05	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    5s.  Last read position: chr5:130,075,753
INFO	2017-01-29 00:33:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:07	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    2s.  Last read position: chr6:85,011,748
INFO	2017-01-29 00:33:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:14	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    6s.  Last read position: chr7:25,928,438
INFO	2017-01-29 00:33:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:19	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    5s.  Last read position: chr8:29,494,320
INFO	2017-01-29 00:33:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:21	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    2s.  Last read position: chr9:110,074,320
INFO	2017-01-29 00:33:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:25	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    4s.  Last read position: chr10:102,605,565
INFO	2017-01-29 00:33:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:28	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    2s.  Last read position: chr11:111,775,832
INFO	2017-01-29 00:33:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:38	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:   10s.  Last read position: chr12:115,709,731
INFO	2017-01-29 00:33:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:41	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    2s.  Last read position: chr14:50,581,951
INFO	2017-01-29 00:33:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:45	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    4s.  Last read position: chr15:95,362,792
INFO	2017-01-29 00:33:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:47	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    2s.  Last read position: chr17:51,144,994
INFO	2017-01-29 00:33:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:33:59	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:   11s.  Last read position: chr19:36,122,074
INFO	2017-01-29 00:33:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:34:02	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    2s.  Last read position: chr22:25,686,705
INFO	2017-01-29 00:34:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:34:05	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    2s.  Last read position: chrX:138,043,024
INFO	2017-01-29 00:34:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:34:05	MarkDuplicates	Read 20137423 records. 0 pairs never matched.
INFO	2017-01-29 00:34:09	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4215976368; totalMemory: 5934940160; maxMemory: 11453595648
INFO	2017-01-29 00:34:09	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:34:10	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:34:10	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:34:11	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:34:31	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5677051312; totalMemory: 8617721856; maxMemory: 11453595648
INFO	2017-01-29 00:34:31	MarkDuplicates	Marking 1257527 records as duplicates.
INFO	2017-01-29 00:34:31	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:35:46	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:14s.  Time for last 10,000,000:   74s.  Last read position: chr8:29,494,320
INFO	2017-01-29 00:37:03	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:31s.  Time for last 10,000,000:   77s.  Last read position: chrX:138,043,024
INFO	2017-01-29 00:37:04	MarkDuplicates	Before output close freeMemory: 8753127120; totalMemory: 8833204224; maxMemory: 11453595648
INFO	2017-01-29 00:37:04	MarkDuplicates	After output close freeMemory: 8599509576; totalMemory: 8679587840; maxMemory: 11453595648
[Sun Jan 29 00:37:05 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.72 minutes.
Runtime.totalMemory()=8679587840

Num	11
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
Name	dedup_bam_2 rep1
Thread	thread_41
PID	35998

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

Start	2017-01-29 00:37:07
End	2017-01-29 00:41:57
Elapsed	00:04:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.bam

# SYS command. line 153

 sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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/H3K4me1/out/qc/rep1/SRR1016001.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--------------------
12422 (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	36004

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

Start	2017-01-29 00:41:58
End	2017-01-29 00:43:22
Elapsed	00:01:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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--------------------
30634 (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	36007

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

Start	2017-01-29 00:43:23
End	2017-01-29 00:44:37
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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--------------------
35166 (process ID) old priority 0, new priority 10
Waiting for 32 seconds.

Num	14
ID	task.postalign_bed.spr_rep1.line_255.id_23
Name	spr rep1
Thread	thread_41
PID	36008

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

Start	2017-01-29 00:43:24
End	2017-01-29 00:44:36
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.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--------------------
35165 (process ID) old priority 0, new priority 10
Waiting for 20 seconds.

Num	15
ID	task.postalign_bed.xcor_rep1.line_212.id_24
Name	xcor rep1
Thread	thread_41
PID	36009

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

Start	2017-01-29 00:44:38
End	2017-01-29 00:53:02
Elapsed	00:08:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.nodup.15M.tagAlign.gz -p=3 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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--------------------
8574 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.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/H3K4me1/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/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.15M.tagAlign.gz 
opened /tmp/36009.1.q/Rtmput1QCr/SRR1016001.nodup.15M.tagAlign21bd511edaf7
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1739784 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.180456788490706,0.17694023835072,0.176753951557191 
Top 3 estimates for fragment length 90,220,235 
Window half size 290 
Phantom peak location 55 
Phantom peak Correlation 0.1785121 
Normalized Strand cross-correlation coefficient (NSC) 1.037237 
Relative Strand cross-correlation Coefficient (RSC) 1.428933 
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	36027

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

Start	2017-01-29 00:53:04
End	2017-01-29 01:17:45
Elapsed	00:24:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/signal/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/signal/macs2/rep1/SRR1016001.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/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 90 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1 -o "SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/signal/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1 -o "SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/signal/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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--------------------
13556 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:53:22: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 00:53:22: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:53:22: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:53:24:  1000000 
INFO  @ Sun, 29 Jan 2017 00:53:26:  2000000 
INFO  @ Sun, 29 Jan 2017 00:53:27:  3000000 
INFO  @ Sun, 29 Jan 2017 00:53:29:  4000000 
INFO  @ Sun, 29 Jan 2017 00:53:30:  5000000 
INFO  @ Sun, 29 Jan 2017 00:53:32:  6000000 
INFO  @ Sun, 29 Jan 2017 00:53:33:  7000000 
INFO  @ Sun, 29 Jan 2017 00:53:35:  8000000 
INFO  @ Sun, 29 Jan 2017 00:53:36:  9000000 
INFO  @ Sun, 29 Jan 2017 00:53:38:  10000000 
INFO  @ Sun, 29 Jan 2017 00:53:39:  11000000 
INFO  @ Sun, 29 Jan 2017 00:53:41:  12000000 
INFO  @ Sun, 29 Jan 2017 00:53:43:  13000000 
INFO  @ Sun, 29 Jan 2017 00:53:44:  14000000 
INFO  @ Sun, 29 Jan 2017 00:53:46:  15000000 
INFO  @ Sun, 29 Jan 2017 00:53:47:  16000000 
INFO  @ Sun, 29 Jan 2017 00:53:49:  17000000 
INFO  @ Sun, 29 Jan 2017 00:53:50:  18000000 
INFO  @ Sun, 29 Jan 2017 00:53:52: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:53:53:  1000000 
INFO  @ Sun, 29 Jan 2017 00:53:55:  2000000 
INFO  @ Sun, 29 Jan 2017 00:53:57:  3000000 
INFO  @ Sun, 29 Jan 2017 00:53:58:  4000000 
INFO  @ Sun, 29 Jan 2017 00:54:00:  5000000 
INFO  @ Sun, 29 Jan 2017 00:54:01:  6000000 
INFO  @ Sun, 29 Jan 2017 00:54:03:  7000000 
INFO  @ Sun, 29 Jan 2017 00:54:04:  8000000 
INFO  @ Sun, 29 Jan 2017 00:54:06:  9000000 
INFO  @ Sun, 29 Jan 2017 00:54:07:  10000000 
INFO  @ Sun, 29 Jan 2017 00:54:09:  11000000 
INFO  @ Sun, 29 Jan 2017 00:54:09: #1 tag size is determined as 50 bps 
INFO  @ Sun, 29 Jan 2017 00:54:09: #1 tag size = 50 
INFO  @ Sun, 29 Jan 2017 00:54:09: #1  total tags in treatment: 18879896 
INFO  @ Sun, 29 Jan 2017 00:54:09: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:54:09: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:54:09: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:54:09: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:54:09: #2 Use 90 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:54:09: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:54:09: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:54:09: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:54:58: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:54:58: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:54:58: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:54:58: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:54:58: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:57:19: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:57:19: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:57:19: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:57:19: Done! 
INFO  @ Sun, 29 Jan 2017 00:57:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 90 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/rep1/SRR1016001.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 00:57:21: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:57:21: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:57:23:  1000000 
INFO  @ Sun, 29 Jan 2017 00:57:24:  2000000 
INFO  @ Sun, 29 Jan 2017 00:57:25:  3000000 
INFO  @ Sun, 29 Jan 2017 00:57:27:  4000000 
INFO  @ Sun, 29 Jan 2017 00:57:28:  5000000 
INFO  @ Sun, 29 Jan 2017 00:57:30:  6000000 
INFO  @ Sun, 29 Jan 2017 00:57:31:  7000000 
INFO  @ Sun, 29 Jan 2017 00:57:32:  8000000 
INFO  @ Sun, 29 Jan 2017 00:57:34:  9000000 
INFO  @ Sun, 29 Jan 2017 00:57:35:  10000000 
INFO  @ Sun, 29 Jan 2017 00:57:37:  11000000 
INFO  @ Sun, 29 Jan 2017 00:57:38:  12000000 
INFO  @ Sun, 29 Jan 2017 00:57:39:  13000000 
INFO  @ Sun, 29 Jan 2017 00:57:41:  14000000 
INFO  @ Sun, 29 Jan 2017 00:57:42:  15000000 
INFO  @ Sun, 29 Jan 2017 00:57:43:  16000000 
INFO  @ Sun, 29 Jan 2017 00:57:45:  17000000 
INFO  @ Sun, 29 Jan 2017 00:57:46:  18000000 
INFO  @ Sun, 29 Jan 2017 00:57:48: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:57:49:  1000000 
INFO  @ Sun, 29 Jan 2017 00:57:50:  2000000 
INFO  @ Sun, 29 Jan 2017 00:57:52:  3000000 
INFO  @ Sun, 29 Jan 2017 00:57:53:  4000000 
INFO  @ Sun, 29 Jan 2017 00:57:55:  5000000 
INFO  @ Sun, 29 Jan 2017 00:57:56:  6000000 
INFO  @ Sun, 29 Jan 2017 00:57:57:  7000000 
INFO  @ Sun, 29 Jan 2017 00:57:59:  8000000 
INFO  @ Sun, 29 Jan 2017 00:58:00:  9000000 
INFO  @ Sun, 29 Jan 2017 00:58:02:  10000000 
INFO  @ Sun, 29 Jan 2017 00:58:03:  11000000 
INFO  @ Sun, 29 Jan 2017 00:58:04: #1 tag size is determined as 50 bps 
INFO  @ Sun, 29 Jan 2017 00:58:04: #1 tag size = 50 
INFO  @ Sun, 29 Jan 2017 00:58:04: #1  total tags in treatment: 18879896 
INFO  @ Sun, 29 Jan 2017 00:58:04: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:58:04: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:58:04: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:58:04: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:58:04: #2 Use 90 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:58:04: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:58:04: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:58:04: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:58:54: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:59:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:59:48: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:59:51: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:59:53: Done! 
INFO  @ Sun, 29 Jan 2017 01:00:03: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:00:43: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:01:23: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 01:01:44: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 29 Jan 2017 01:04:16: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 01:05:51: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Sun, 29 Jan 2017 01:09:16: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:09:53: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:10:30: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 01:10:50: Values in your input bedGraph files will be multiplied by 11.201413 ... 
INFO  @ Sun, 29 Jan 2017 01:13:22: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Sun, 29 Jan 2017 01:13:40: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 01:14:51: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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	36028

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

Start	2017-01-29 00:53:05
End	2017-01-29 00:59:28
Elapsed	00:06:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 90 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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--------------------
13554 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:53:22: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 00:53:22: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:53:22: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:53:24:  1000000 
INFO  @ Sun, 29 Jan 2017 00:53:26:  2000000 
INFO  @ Sun, 29 Jan 2017 00:53:27:  3000000 
INFO  @ Sun, 29 Jan 2017 00:53:29:  4000000 
INFO  @ Sun, 29 Jan 2017 00:53:30:  5000000 
INFO  @ Sun, 29 Jan 2017 00:53:32:  6000000 
INFO  @ Sun, 29 Jan 2017 00:53:33:  7000000 
INFO  @ Sun, 29 Jan 2017 00:53:35:  8000000 
INFO  @ Sun, 29 Jan 2017 00:53:36:  9000000 
INFO  @ Sun, 29 Jan 2017 00:53:37: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:53:39:  1000000 
INFO  @ Sun, 29 Jan 2017 00:53:40:  2000000 
INFO  @ Sun, 29 Jan 2017 00:53:42:  3000000 
INFO  @ Sun, 29 Jan 2017 00:53:43:  4000000 
INFO  @ Sun, 29 Jan 2017 00:53:44:  5000000 
INFO  @ Sun, 29 Jan 2017 00:53:46:  6000000 
INFO  @ Sun, 29 Jan 2017 00:53:47:  7000000 
INFO  @ Sun, 29 Jan 2017 00:53:48:  8000000 
INFO  @ Sun, 29 Jan 2017 00:53:50:  9000000 
INFO  @ Sun, 29 Jan 2017 00:53:51:  10000000 
INFO  @ Sun, 29 Jan 2017 00:53:53:  11000000 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1 tag size is determined as 50 bps 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1 tag size = 50 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1  total tags in treatment: 9439948 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:53:53: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #2 Use 90 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:53:53: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:56:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:56:22: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:56:23: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:56:24: Done! 
INFO  @ Sun, 29 Jan 2017 00:56:27: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 90 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 00:56:27: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:56:27: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:56:28:  1000000 
INFO  @ Sun, 29 Jan 2017 00:56:30:  2000000 
INFO  @ Sun, 29 Jan 2017 00:56:32:  3000000 
INFO  @ Sun, 29 Jan 2017 00:56:33:  4000000 
INFO  @ Sun, 29 Jan 2017 00:56:35:  5000000 
INFO  @ Sun, 29 Jan 2017 00:56:37:  6000000 
INFO  @ Sun, 29 Jan 2017 00:56:38:  7000000 
INFO  @ Sun, 29 Jan 2017 00:56:40:  8000000 
INFO  @ Sun, 29 Jan 2017 00:56:41:  9000000 
INFO  @ Sun, 29 Jan 2017 00:56:42: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:56:44:  1000000 
INFO  @ Sun, 29 Jan 2017 00:56:45:  2000000 
INFO  @ Sun, 29 Jan 2017 00:56:47:  3000000 
INFO  @ Sun, 29 Jan 2017 00:56:48:  4000000 
INFO  @ Sun, 29 Jan 2017 00:56:50:  5000000 
INFO  @ Sun, 29 Jan 2017 00:56:51:  6000000 
INFO  @ Sun, 29 Jan 2017 00:56:53:  7000000 
INFO  @ Sun, 29 Jan 2017 00:56:55:  8000000 
INFO  @ Sun, 29 Jan 2017 00:56:56:  9000000 
INFO  @ Sun, 29 Jan 2017 00:56:57:  10000000 
INFO  @ Sun, 29 Jan 2017 00:56:59:  11000000 
INFO  @ Sun, 29 Jan 2017 00:56:59: #1 tag size is determined as 50 bps 
INFO  @ Sun, 29 Jan 2017 00:56:59: #1 tag size = 50 
INFO  @ Sun, 29 Jan 2017 00:56:59: #1  total tags in treatment: 9439948 
INFO  @ Sun, 29 Jan 2017 00:56:59: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:56:59: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:56:59: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:56:59: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:56:59: #2 Use 90 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:56:59: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:56:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:56:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:57:40: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:58:52: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:59:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:59:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:59:10: Done!

Num	18
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27
Name	macs2 rep1-pr2
Thread	thread_Root
PID	36029

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

Start	2017-01-29 00:53:06
End	2017-01-29 00:59:33
Elapsed	00:06:27
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 90 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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--------------------
13555 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:53:22: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 00:53:22: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:53:22: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:53:24:  1000000 
INFO  @ Sun, 29 Jan 2017 00:53:25:  2000000 
INFO  @ Sun, 29 Jan 2017 00:53:27:  3000000 
INFO  @ Sun, 29 Jan 2017 00:53:28:  4000000 
INFO  @ Sun, 29 Jan 2017 00:53:30:  5000000 
INFO  @ Sun, 29 Jan 2017 00:53:31:  6000000 
INFO  @ Sun, 29 Jan 2017 00:53:33:  7000000 
INFO  @ Sun, 29 Jan 2017 00:53:34:  8000000 
INFO  @ Sun, 29 Jan 2017 00:53:36:  9000000 
INFO  @ Sun, 29 Jan 2017 00:53:37: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:53:38:  1000000 
INFO  @ Sun, 29 Jan 2017 00:53:40:  2000000 
INFO  @ Sun, 29 Jan 2017 00:53:41:  3000000 
INFO  @ Sun, 29 Jan 2017 00:53:43:  4000000 
INFO  @ Sun, 29 Jan 2017 00:53:44:  5000000 
INFO  @ Sun, 29 Jan 2017 00:53:45:  6000000 
INFO  @ Sun, 29 Jan 2017 00:53:47:  7000000 
INFO  @ Sun, 29 Jan 2017 00:53:48:  8000000 
INFO  @ Sun, 29 Jan 2017 00:53:50:  9000000 
INFO  @ Sun, 29 Jan 2017 00:53:51:  10000000 
INFO  @ Sun, 29 Jan 2017 00:53:52:  11000000 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1 tag size is determined as 49 bps 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1 tag size = 49 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1  total tags in treatment: 9439948 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:53:53: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:53:53: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #2 Use 90 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:53:53: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:53:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:54:33: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:56:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:56:24: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:56:25: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:56:26: Done! 
INFO  @ Sun, 29 Jan 2017 00:56:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 90 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 00:56:29: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:56:29: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:56:30:  1000000 
INFO  @ Sun, 29 Jan 2017 00:56:32:  2000000 
INFO  @ Sun, 29 Jan 2017 00:56:34:  3000000 
INFO  @ Sun, 29 Jan 2017 00:56:35:  4000000 
INFO  @ Sun, 29 Jan 2017 00:56:37:  5000000 
INFO  @ Sun, 29 Jan 2017 00:56:38:  6000000 
INFO  @ Sun, 29 Jan 2017 00:56:40:  7000000 
INFO  @ Sun, 29 Jan 2017 00:56:41:  8000000 
INFO  @ Sun, 29 Jan 2017 00:56:43:  9000000 
INFO  @ Sun, 29 Jan 2017 00:56:44: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:56:45:  1000000 
INFO  @ Sun, 29 Jan 2017 00:56:47:  2000000 
INFO  @ Sun, 29 Jan 2017 00:56:48:  3000000 
INFO  @ Sun, 29 Jan 2017 00:56:50:  4000000 
INFO  @ Sun, 29 Jan 2017 00:56:51:  5000000 
INFO  @ Sun, 29 Jan 2017 00:56:52:  6000000 
INFO  @ Sun, 29 Jan 2017 00:56:54:  7000000 
INFO  @ Sun, 29 Jan 2017 00:56:55:  8000000 
INFO  @ Sun, 29 Jan 2017 00:56:57:  9000000 
INFO  @ Sun, 29 Jan 2017 00:56:58:  10000000 
INFO  @ Sun, 29 Jan 2017 00:56:59:  11000000 
INFO  @ Sun, 29 Jan 2017 00:57:00: #1 tag size is determined as 49 bps 
INFO  @ Sun, 29 Jan 2017 00:57:00: #1 tag size = 49 
INFO  @ Sun, 29 Jan 2017 00:57:00: #1  total tags in treatment: 9439948 
INFO  @ Sun, 29 Jan 2017 00:57:00: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:57:00: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:57:00: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:57:00: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:57:00: #2 Use 90 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:57:00: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:57:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:57:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:57:43: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:58:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:59:05: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:59:10: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:59:15: Done!

Num	19
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28
Name	naive_overlap_thresh
Thread	thread_Root
PID	36050

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

Start	2017-01-29 01:17:47
End	2017-01-29 01:19:06
Elapsed	00:01:19
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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--------------------
9268 (process ID) old priority 0, new priority 10
Waiting for 56 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr3	141384666	141385043	Peak_2	180	.	10.64910	18.09799	9.41568	67

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr3	141384666	141385043	Peak_2	180	.	10.64910	18.09799	9.41568	67

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
chr16	34582172	34582314	Peak_2	244	.	12.48137	24.47197	16.39401	76

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
chr16	34582172	34582314	Peak_2	244	.	12.48137	24.47197	16.39401	76

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1	66816	66909	Peak_10971	32	.	3.46649	3.22608	0.00000	77

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1	66816	66909	Peak_10971	32	.	3.46649	3.22608	0.00000	77

Num	20
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29
Name	naive_overlap_thresh
Thread	thread_Root
PID	36051

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

Start	2017-01-29 01:17:48
End	2017-01-29 01:19:06
Elapsed	00:01:18
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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--------------------
9267 (process ID) old priority 0, new priority 10
Waiting for 25 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr16	83214275	83214365	Peak_8	37	.	83214275	83214365	0	2	1,1	0,89	6.44017	9.55972	3.75078

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr16	83214275	83214365	Peak_8	37	.	83214275	83214365	0	2	1,1	0,89	6.44017	9.55972	3.75078

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
chr16	83398580	83398670	Peak_3	109	.	83398580	83398670	0	2	1,1	0,89	10.64910	18.09799	10.91893

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
chr16	83398580	83398670	Peak_3	109	.	83398580	83398670	0	2	1,1	0,89	10.64910	18.09799	10.91893

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1	121742	121993	Peak_17850	0	.	121742	121993	0	2	1,1	0,250	2.01517	1.66449	0.00000

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1	121742	121993	Peak_17850	0	.	121742	121993	0	2	1,1	0,250	2.01517	1.66449	0.00000

Num	21
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30
Name	naive_overlap_thresh
Thread	thread_Root
PID	36052

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

Start	2017-01-29 01:17:49
End	2017-01-29 01:19:07
Elapsed	00:01:17
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016001.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/H3K4me1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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--------------------
9269 (process ID) old priority 0, new priority 10
Waiting for 34 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr16	83214275	83214365	Peak_8	37	.	6.44017	9.55972	3.75078

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr16	83214275	83214365	Peak_8	37	.	6.44017	9.55972	3.75078

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
chr16	83398580	83398670	Peak_3	109	.	10.64910	18.09799	10.91893

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
chr16	83398580	83398670	Peak_3	109	.	10.64910	18.09799	10.91893

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1	121742	121993	Peak_17850	0	.	2.01517	1.66449	0.00000

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1	121742	121993	Peak_17850	0	.	2.01517	1.66449	0.00000

Num	22
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31
Name	blacklist_filter peak 1
Thread	thread_Root
PID	49556

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

Start	2017-01-29 01:19:09
End	2017-01-29 01:20:18
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.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/H3K4me1/out/peak/macs2/rep1/SRR1016001.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--------------------
49560 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000225.1	50824	50972	Peak_1	255	.	12.88769	25.57209	16.07824	71

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/rep1/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000225.1	50824	50972	Peak_1	255	.	12.88769	25.57209	16.07824	71

Num	23
ID	task.report.peak2hammock.line_412.id_32
Name	peak2hammock
Thread	thread_Root
PID	53773

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

Start	2017-01-29 01:20:19
End	2017-01-29 01:20:28
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
53777 (process ID) old priority 0, new priority 10

Num	24
ID	task.report.peak2hammock.line_412.id_33
Name	peak2hammock
Thread	thread_Root
PID	54443

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

Start	2017-01-29 01:20:29
End	2017-01-29 01:20:48
Elapsed	00:00:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.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/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/peak/macs2/overlap/SRR1016001.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
54447 (process ID) old priority 0, new priority 10

Num	25
ID	task.graphviz.report.line_97.id_34
Name	report
Thread	thread_Root
PID	55895

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

Start	2017-01-29 01:20:49
End	2017-01-29 01:20:57
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/H3K4me1/out/report/H3K4me1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/report/H3K4me1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/report/H3K4me1_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
55901 (process ID) old priority 0, new priority 10

Num	26
ID	task.report.pdf2png.line_379.id_39
Name	pdf2png
Thread	thread_Root
PID	55900

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

Start	2017-01-29 01:20:49
End	2017-01-29 01:20:57
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.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/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me1/out/qc/rep1/SRR1016001.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
55909 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, H3K4me1, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016001.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/H3K4me1
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/H3K4me1
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	24711.H3K4me1.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

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