Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170125_140849_075
Start time	2017-01-25 14:08:49
Run time	00:39:18.086
Tasks executed	15
Tasks failed	0
Tasks failed names
Arguments*	[-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep1/ENCFF002AAV.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep2/ENCFF002AAW.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes, -no_pseudo_rep, -histone, -out_dir, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170125_140849_075/task.postalign_bed.pool_tag_pooled_rep.line_436.id_10 chipseq.bds.20170125_140849_075/task.postalign_bed.pool_tag_ppr1.line_436.id_11 chipseq.bds.20170125_140849_075/task.postalign_bed.pool_tag_ppr2.line_436.id_12 chipseq.bds.20170125_140849_075/task.callpeak_macs2.macs2_pooled_rep.line_71.id_13 chipseq.bds.20170125_140849_075/task.callpeak_macs2.macs2_ppr1.line_71.id_14 chipseq.bds.20170125_140849_075/task.callpeak_macs2.macs2_ppr2.line_71.id_15 chipseq.bds.20170125_140849_075/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16 chipseq.bds.20170125_140849_075/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17 chipseq.bds.20170125_140849_075/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_18 chipseq.bds.20170125_140849_075/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_19 chipseq.bds.20170125_140849_075/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_20 chipseq.bds.20170125_140849_075/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_21 chipseq.bds.20170125_140849_075/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170125_140849_075/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170125_140849_075/task.graphviz.report.line_97.id_24
thread_42	thread_Root
thread_41	thread_Root
thread_43	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.postalign_bed.pool_tag_pooled_rep.line_436.id_10
Name	pool_tag pooled_rep
Thread	thread_Root
PID	35520

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

Start	2017-01-25 14:08:59
End	2017-01-25 14:10:23
Elapsed	00:01:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep1/ENCFF002AAV.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep2/ENCFF002AAW.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 438

 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 440

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep1/ENCFF002AAV.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep2/ENCFF002AAW.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz

# SYS command. line 442

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
23183 (process ID) old priority 0, new priority 10
Waiting for 20 seconds.

Num	2
ID	task.postalign_bed.pool_tag_ppr1.line_436.id_11
Name	pool_tag ppr1
Thread	thread_Root
PID	35521

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

Start	2017-01-25 14:08:59
End	2017-01-25 14:10:23
Elapsed	00:01:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep1/pr1/ENCFF002AAV.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep2/pr1/ENCFF002AAW.nodup.pr1.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz
Dependencies

 
# SYS command. line 438

 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 440

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep1/pr1/ENCFF002AAV.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep2/pr1/ENCFF002AAW.nodup.pr1.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz

# SYS command. line 442

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
23182 (process ID) old priority 0, new priority 10
Waiting for 36 seconds.

Num	3
ID	task.postalign_bed.pool_tag_ppr2.line_436.id_12
Name	pool_tag ppr2
Thread	thread_Root
PID	35522

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

Start	2017-01-25 14:09:00
End	2017-01-25 14:10:22
Elapsed	00:01:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep1/pr2/ENCFF002AAV.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep2/pr2/ENCFF002AAW.nodup.pr2.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz
Dependencies

 
# SYS command. line 438

 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 440

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep1/pr2/ENCFF002AAV.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pseudo_reps/rep2/pr2/ENCFF002AAW.nodup.pr2.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz

# SYS command. line 442

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
23184 (process ID) old priority 0, new priority 10
Waiting for 36 seconds.

Num	4
ID	task.callpeak_macs2.macs2_pooled_rep.line_71.id_13
Name	macs2 pooled_rep
Thread	thread_Root
PID	35523

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

Start	2017-01-25 14:10:24
End	2017-01-25 14:44:59
Elapsed	00:34:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/signal/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/signal/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep -o "ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/signal/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep -o "ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/signal/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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--------------------
11715 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 14:10:40: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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  @ Wed, 25 Jan 2017 14:10:40: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 14:10:40: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 14:10:42:  1000000 
INFO  @ Wed, 25 Jan 2017 14:10:43:  2000000 
INFO  @ Wed, 25 Jan 2017 14:10:44:  3000000 
INFO  @ Wed, 25 Jan 2017 14:10:46:  4000000 
INFO  @ Wed, 25 Jan 2017 14:10:47:  5000000 
INFO  @ Wed, 25 Jan 2017 14:10:48:  6000000 
INFO  @ Wed, 25 Jan 2017 14:10:50:  7000000 
INFO  @ Wed, 25 Jan 2017 14:10:51:  8000000 
INFO  @ Wed, 25 Jan 2017 14:10:52:  9000000 
INFO  @ Wed, 25 Jan 2017 14:10:53:  10000000 
INFO  @ Wed, 25 Jan 2017 14:10:55:  11000000 
INFO  @ Wed, 25 Jan 2017 14:10:56:  12000000 
INFO  @ Wed, 25 Jan 2017 14:10:57:  13000000 
INFO  @ Wed, 25 Jan 2017 14:10:59:  14000000 
INFO  @ Wed, 25 Jan 2017 14:11:00:  15000000 
INFO  @ Wed, 25 Jan 2017 14:11:01:  16000000 
INFO  @ Wed, 25 Jan 2017 14:11:03:  17000000 
INFO  @ Wed, 25 Jan 2017 14:11:04:  18000000 
INFO  @ Wed, 25 Jan 2017 14:11:05:  19000000 
INFO  @ Wed, 25 Jan 2017 14:11:07:  20000000 
INFO  @ Wed, 25 Jan 2017 14:11:08:  21000000 
INFO  @ Wed, 25 Jan 2017 14:11:09:  22000000 
INFO  @ Wed, 25 Jan 2017 14:11:11:  23000000 
INFO  @ Wed, 25 Jan 2017 14:11:12:  24000000 
INFO  @ Wed, 25 Jan 2017 14:11:13:  25000000 
INFO  @ Wed, 25 Jan 2017 14:11:15:  26000000 
INFO  @ Wed, 25 Jan 2017 14:11:16:  27000000 
INFO  @ Wed, 25 Jan 2017 14:11:18:  28000000 
INFO  @ Wed, 25 Jan 2017 14:11:19:  29000000 
INFO  @ Wed, 25 Jan 2017 14:11:20:  30000000 
INFO  @ Wed, 25 Jan 2017 14:11:21:  31000000 
INFO  @ Wed, 25 Jan 2017 14:11:23:  32000000 
INFO  @ Wed, 25 Jan 2017 14:11:24: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 14:11:26:  1000000 
INFO  @ Wed, 25 Jan 2017 14:11:27:  2000000 
INFO  @ Wed, 25 Jan 2017 14:11:28:  3000000 
INFO  @ Wed, 25 Jan 2017 14:11:30:  4000000 
INFO  @ Wed, 25 Jan 2017 14:11:31:  5000000 
INFO  @ Wed, 25 Jan 2017 14:11:32:  6000000 
INFO  @ Wed, 25 Jan 2017 14:11:34:  7000000 
INFO  @ Wed, 25 Jan 2017 14:11:35:  8000000 
INFO  @ Wed, 25 Jan 2017 14:11:36:  9000000 
INFO  @ Wed, 25 Jan 2017 14:11:38:  10000000 
INFO  @ Wed, 25 Jan 2017 14:11:39:  11000000 
INFO  @ Wed, 25 Jan 2017 14:11:40: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 14:11:40: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 14:11:40: #1  total tags in treatment: 32548757 
INFO  @ Wed, 25 Jan 2017 14:11:40: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 14:11:40: #1 finished! 
INFO  @ Wed, 25 Jan 2017 14:11:40: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 14:11:40: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 14:11:40: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 14:11:40: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 14:11:40: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 14:11:40: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 14:12:47: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 14:12:47: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 14:12:47: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 14:12:47: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 14:12:47: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 14:16:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 14:16:08: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 14:16:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 14:16:09: Done! 
INFO  @ Wed, 25 Jan 2017 14:16:12: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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  @ Wed, 25 Jan 2017 14:16:12: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 14:16:12: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 14:16:14:  1000000 
INFO  @ Wed, 25 Jan 2017 14:16:16:  2000000 
INFO  @ Wed, 25 Jan 2017 14:16:17:  3000000 
INFO  @ Wed, 25 Jan 2017 14:16:19:  4000000 
INFO  @ Wed, 25 Jan 2017 14:16:20:  5000000 
INFO  @ Wed, 25 Jan 2017 14:16:22:  6000000 
INFO  @ Wed, 25 Jan 2017 14:16:24:  7000000 
INFO  @ Wed, 25 Jan 2017 14:16:25:  8000000 
INFO  @ Wed, 25 Jan 2017 14:16:27:  9000000 
INFO  @ Wed, 25 Jan 2017 14:16:28:  10000000 
INFO  @ Wed, 25 Jan 2017 14:16:29:  11000000 
INFO  @ Wed, 25 Jan 2017 14:16:31:  12000000 
INFO  @ Wed, 25 Jan 2017 14:16:32:  13000000 
INFO  @ Wed, 25 Jan 2017 14:16:34:  14000000 
INFO  @ Wed, 25 Jan 2017 14:16:36:  15000000 
INFO  @ Wed, 25 Jan 2017 14:16:37:  16000000 
INFO  @ Wed, 25 Jan 2017 14:16:39:  17000000 
INFO  @ Wed, 25 Jan 2017 14:16:40:  18000000 
INFO  @ Wed, 25 Jan 2017 14:16:42:  19000000 
INFO  @ Wed, 25 Jan 2017 14:16:43:  20000000 
INFO  @ Wed, 25 Jan 2017 14:16:45:  21000000 
INFO  @ Wed, 25 Jan 2017 14:16:46:  22000000 
INFO  @ Wed, 25 Jan 2017 14:16:48:  23000000 
INFO  @ Wed, 25 Jan 2017 14:16:50:  24000000 
INFO  @ Wed, 25 Jan 2017 14:16:52:  25000000 
INFO  @ Wed, 25 Jan 2017 14:16:53:  26000000 
INFO  @ Wed, 25 Jan 2017 14:16:55:  27000000 
INFO  @ Wed, 25 Jan 2017 14:16:56:  28000000 
INFO  @ Wed, 25 Jan 2017 14:16:58:  29000000 
INFO  @ Wed, 25 Jan 2017 14:17:00:  30000000 
INFO  @ Wed, 25 Jan 2017 14:17:01:  31000000 
INFO  @ Wed, 25 Jan 2017 14:17:03:  32000000 
INFO  @ Wed, 25 Jan 2017 14:17:04: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 14:17:06:  1000000 
INFO  @ Wed, 25 Jan 2017 14:17:08:  2000000 
INFO  @ Wed, 25 Jan 2017 14:17:09:  3000000 
INFO  @ Wed, 25 Jan 2017 14:17:11:  4000000 
INFO  @ Wed, 25 Jan 2017 14:17:12:  5000000 
INFO  @ Wed, 25 Jan 2017 14:17:14:  6000000 
INFO  @ Wed, 25 Jan 2017 14:17:16:  7000000 
INFO  @ Wed, 25 Jan 2017 14:17:17:  8000000 
INFO  @ Wed, 25 Jan 2017 14:17:19:  9000000 
INFO  @ Wed, 25 Jan 2017 14:17:21:  10000000 
INFO  @ Wed, 25 Jan 2017 14:17:23:  11000000 
INFO  @ Wed, 25 Jan 2017 14:17:24: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 14:17:24: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 14:17:24: #1  total tags in treatment: 32548757 
INFO  @ Wed, 25 Jan 2017 14:17:24: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 14:17:24: #1 finished! 
INFO  @ Wed, 25 Jan 2017 14:17:24: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 14:17:24: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 14:17:24: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 14:17:24: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 14:17:24: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 14:17:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 14:18:29: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 14:19:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 14:19:23: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 14:19:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 14:19:25: Done! 
INFO  @ Wed, 25 Jan 2017 14:19:32: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 14:20:33: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 14:21:05: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 14:21:42: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 14:25:20: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 14:27:50: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 14:34:19: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 14:35:22: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 14:35:53: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 14:36:18: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 14:40:14: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 14:40:38: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 14:41:50: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'!

Num	5
ID	task.callpeak_macs2.macs2_ppr1.line_71.id_14
Name	macs2 ppr1
Thread	thread_Root
PID	35524

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

Start	2017-01-25 14:10:25
End	2017-01-25 14:18:03
Elapsed	00:07:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF002AAV.nodup.pr1_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.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--------------------
23759 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 14:10:41: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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  @ Wed, 25 Jan 2017 14:10:41: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 14:10:41: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 14:10:42:  1000000 
INFO  @ Wed, 25 Jan 2017 14:10:44:  2000000 
INFO  @ Wed, 25 Jan 2017 14:10:46:  3000000 
INFO  @ Wed, 25 Jan 2017 14:10:47:  4000000 
INFO  @ Wed, 25 Jan 2017 14:10:49:  5000000 
INFO  @ Wed, 25 Jan 2017 14:10:52:  6000000 
INFO  @ Wed, 25 Jan 2017 14:10:54:  7000000 
INFO  @ Wed, 25 Jan 2017 14:10:55:  8000000 
INFO  @ Wed, 25 Jan 2017 14:10:57:  9000000 
INFO  @ Wed, 25 Jan 2017 14:10:59:  10000000 
INFO  @ Wed, 25 Jan 2017 14:11:01:  11000000 
INFO  @ Wed, 25 Jan 2017 14:11:03:  12000000 
INFO  @ Wed, 25 Jan 2017 14:11:04:  13000000 
INFO  @ Wed, 25 Jan 2017 14:11:07:  14000000 
INFO  @ Wed, 25 Jan 2017 14:11:08:  15000000 
INFO  @ Wed, 25 Jan 2017 14:11:10:  16000000 
INFO  @ Wed, 25 Jan 2017 14:11:12: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 14:11:13:  1000000 
INFO  @ Wed, 25 Jan 2017 14:11:15:  2000000 
INFO  @ Wed, 25 Jan 2017 14:11:16:  3000000 
INFO  @ Wed, 25 Jan 2017 14:11:18:  4000000 
INFO  @ Wed, 25 Jan 2017 14:11:19:  5000000 
INFO  @ Wed, 25 Jan 2017 14:11:21:  6000000 
INFO  @ Wed, 25 Jan 2017 14:11:23:  7000000 
INFO  @ Wed, 25 Jan 2017 14:11:24:  8000000 
INFO  @ Wed, 25 Jan 2017 14:11:26:  9000000 
INFO  @ Wed, 25 Jan 2017 14:11:28:  10000000 
INFO  @ Wed, 25 Jan 2017 14:11:29:  11000000 
INFO  @ Wed, 25 Jan 2017 14:11:30: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 14:11:30: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 14:11:30: #1  total tags in treatment: 16274379 
INFO  @ Wed, 25 Jan 2017 14:11:30: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 14:11:30: #1 finished! 
INFO  @ Wed, 25 Jan 2017 14:11:30: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 14:11:30: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 14:11:30: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 14:11:30: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 14:11:30: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 14:11:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 14:14:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 14:14:58: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 14:14:58: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 14:14:59: Done! 
INFO  @ Wed, 25 Jan 2017 14:15:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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  @ Wed, 25 Jan 2017 14:15:02: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 14:15:02: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 14:15:05:  1000000 
INFO  @ Wed, 25 Jan 2017 14:15:07:  2000000 
INFO  @ Wed, 25 Jan 2017 14:15:08:  3000000 
INFO  @ Wed, 25 Jan 2017 14:15:10:  4000000 
INFO  @ Wed, 25 Jan 2017 14:15:12:  5000000 
INFO  @ Wed, 25 Jan 2017 14:15:14:  6000000 
INFO  @ Wed, 25 Jan 2017 14:15:16:  7000000 
INFO  @ Wed, 25 Jan 2017 14:15:17:  8000000 
INFO  @ Wed, 25 Jan 2017 14:15:19:  9000000 
INFO  @ Wed, 25 Jan 2017 14:15:20:  10000000 
INFO  @ Wed, 25 Jan 2017 14:15:22:  11000000 
INFO  @ Wed, 25 Jan 2017 14:15:24:  12000000 
INFO  @ Wed, 25 Jan 2017 14:15:26:  13000000 
INFO  @ Wed, 25 Jan 2017 14:15:28:  14000000 
INFO  @ Wed, 25 Jan 2017 14:15:29:  15000000 
INFO  @ Wed, 25 Jan 2017 14:15:31:  16000000 
INFO  @ Wed, 25 Jan 2017 14:15:33: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 14:15:34:  1000000 
INFO  @ Wed, 25 Jan 2017 14:15:36:  2000000 
INFO  @ Wed, 25 Jan 2017 14:15:37:  3000000 
INFO  @ Wed, 25 Jan 2017 14:15:39:  4000000 
INFO  @ Wed, 25 Jan 2017 14:15:40:  5000000 
INFO  @ Wed, 25 Jan 2017 14:15:42:  6000000 
INFO  @ Wed, 25 Jan 2017 14:15:44:  7000000 
INFO  @ Wed, 25 Jan 2017 14:15:45:  8000000 
INFO  @ Wed, 25 Jan 2017 14:15:47:  9000000 
INFO  @ Wed, 25 Jan 2017 14:15:49:  10000000 
INFO  @ Wed, 25 Jan 2017 14:15:50:  11000000 
INFO  @ Wed, 25 Jan 2017 14:15:51: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 14:15:51: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 14:15:51: #1  total tags in treatment: 16274379 
INFO  @ Wed, 25 Jan 2017 14:15:51: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 14:15:51: #1 finished! 
INFO  @ Wed, 25 Jan 2017 14:15:51: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 14:15:51: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 14:15:51: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 14:15:51: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 14:15:51: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 14:15:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 14:16:51: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 14:17:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 14:17:52: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 14:17:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 14:17:56: Done!

Num	6
ID	task.callpeak_macs2.macs2_ppr2.line_71.id_15
Name	macs2 ppr2
Thread	thread_Root
PID	35525

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

Start	2017-01-25 14:10:26
End	2017-01-25 14:18:03
Elapsed	00:07:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF002AAV.nodup.pr2_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.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--------------------
23758 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 14:10:40: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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  @ Wed, 25 Jan 2017 14:10:40: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 14:10:40: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 14:10:42:  1000000 
INFO  @ Wed, 25 Jan 2017 14:10:44:  2000000 
INFO  @ Wed, 25 Jan 2017 14:10:46:  3000000 
INFO  @ Wed, 25 Jan 2017 14:10:48:  4000000 
INFO  @ Wed, 25 Jan 2017 14:10:49:  5000000 
INFO  @ Wed, 25 Jan 2017 14:10:51:  6000000 
INFO  @ Wed, 25 Jan 2017 14:10:53:  7000000 
INFO  @ Wed, 25 Jan 2017 14:10:55:  8000000 
INFO  @ Wed, 25 Jan 2017 14:10:56:  9000000 
INFO  @ Wed, 25 Jan 2017 14:10:58:  10000000 
INFO  @ Wed, 25 Jan 2017 14:11:00:  11000000 
INFO  @ Wed, 25 Jan 2017 14:11:01:  12000000 
INFO  @ Wed, 25 Jan 2017 14:11:03:  13000000 
INFO  @ Wed, 25 Jan 2017 14:11:05:  14000000 
INFO  @ Wed, 25 Jan 2017 14:11:06:  15000000 
INFO  @ Wed, 25 Jan 2017 14:11:08:  16000000 
INFO  @ Wed, 25 Jan 2017 14:11:09: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 14:11:11:  1000000 
INFO  @ Wed, 25 Jan 2017 14:11:13:  2000000 
INFO  @ Wed, 25 Jan 2017 14:11:14:  3000000 
INFO  @ Wed, 25 Jan 2017 14:11:16:  4000000 
INFO  @ Wed, 25 Jan 2017 14:11:18:  5000000 
INFO  @ Wed, 25 Jan 2017 14:11:20:  6000000 
INFO  @ Wed, 25 Jan 2017 14:11:21:  7000000 
INFO  @ Wed, 25 Jan 2017 14:11:23:  8000000 
INFO  @ Wed, 25 Jan 2017 14:11:24:  9000000 
INFO  @ Wed, 25 Jan 2017 14:11:26:  10000000 
INFO  @ Wed, 25 Jan 2017 14:11:28:  11000000 
INFO  @ Wed, 25 Jan 2017 14:11:28: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 14:11:28: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 14:11:28: #1  total tags in treatment: 16274378 
INFO  @ Wed, 25 Jan 2017 14:11:28: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 14:11:28: #1 finished! 
INFO  @ Wed, 25 Jan 2017 14:11:28: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 14:11:28: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 14:11:28: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 14:11:28: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 14:11:28: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 14:11:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 14:12:29: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 14:14:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 14:14:57: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 14:14:58: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 14:14:58: Done! 
INFO  @ Wed, 25 Jan 2017 14:15:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/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  @ Wed, 25 Jan 2017 14:15:02: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 14:15:02: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 14:15:04:  1000000 
INFO  @ Wed, 25 Jan 2017 14:15:06:  2000000 
INFO  @ Wed, 25 Jan 2017 14:15:08:  3000000 
INFO  @ Wed, 25 Jan 2017 14:15:10:  4000000 
INFO  @ Wed, 25 Jan 2017 14:15:11:  5000000 
INFO  @ Wed, 25 Jan 2017 14:15:13:  6000000 
INFO  @ Wed, 25 Jan 2017 14:15:15:  7000000 
INFO  @ Wed, 25 Jan 2017 14:15:16:  8000000 
INFO  @ Wed, 25 Jan 2017 14:15:18:  9000000 
INFO  @ Wed, 25 Jan 2017 14:15:20:  10000000 
INFO  @ Wed, 25 Jan 2017 14:15:22:  11000000 
INFO  @ Wed, 25 Jan 2017 14:15:23:  12000000 
INFO  @ Wed, 25 Jan 2017 14:15:25:  13000000 
INFO  @ Wed, 25 Jan 2017 14:15:27:  14000000 
INFO  @ Wed, 25 Jan 2017 14:15:29:  15000000 
INFO  @ Wed, 25 Jan 2017 14:15:30:  16000000 
INFO  @ Wed, 25 Jan 2017 14:15:32: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 14:15:33:  1000000 
INFO  @ Wed, 25 Jan 2017 14:15:35:  2000000 
INFO  @ Wed, 25 Jan 2017 14:15:37:  3000000 
INFO  @ Wed, 25 Jan 2017 14:15:38:  4000000 
INFO  @ Wed, 25 Jan 2017 14:15:40:  5000000 
INFO  @ Wed, 25 Jan 2017 14:15:41:  6000000 
INFO  @ Wed, 25 Jan 2017 14:15:43:  7000000 
INFO  @ Wed, 25 Jan 2017 14:15:44:  8000000 
INFO  @ Wed, 25 Jan 2017 14:15:46:  9000000 
INFO  @ Wed, 25 Jan 2017 14:15:47:  10000000 
INFO  @ Wed, 25 Jan 2017 14:15:49:  11000000 
INFO  @ Wed, 25 Jan 2017 14:15:50: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 14:15:50: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 14:15:50: #1  total tags in treatment: 16274378 
INFO  @ Wed, 25 Jan 2017 14:15:50: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 14:15:50: #1 finished! 
INFO  @ Wed, 25 Jan 2017 14:15:50: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 14:15:50: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 14:15:50: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 14:15:50: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 14:15:50: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 14:15:50: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 14:16:51: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 14:17:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 14:17:52: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 14:17:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 14:17:56: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	35551

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

Start	2017-01-25 14:45:01
End	2017-01-25 14:46:23
Elapsed	00:01:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
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 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
31635 (process ID) old priority 0, new priority 10
Waiting for 55 seconds.

Num	8
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17
Name	naive_overlap_thresh
Thread	thread_Root
PID	35552

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

Start	2017-01-25 14:45:01
End	2017-01-25 14:46:22
Elapsed	00:01:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
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 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
31633 (process ID) old priority 0, new priority 10
Waiting for 41 seconds.

Num	9
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_18
Name	naive_overlap_thresh
Thread	thread_Root
PID	35553

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

Start	2017-01-25 14:45:02
End	2017-01-25 14:46:22
Elapsed	00:01:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
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 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAV.nodup.pr1_ENCFF002AAW.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAV.nodup.pr2_ENCFF002AAW.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
31634 (process ID) old priority 0, new priority 10
Waiting for 47 seconds.

Num	10
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_19
Name	blacklist_filter peak_pooled
Thread	thread_Root
PID	51808

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

Start	2017-01-25 14:46:25
End	2017-01-25 14:47:33
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/pooled_rep/ENCFF002AAV.nodup_ENCFF002AAW.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--------------------
51812 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	11
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_20
Name	blacklist_filter peak 1
Thread	thread_Root
PID	51858

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

Start	2017-01-25 14:46:26
End	2017-01-25 14:47:33
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep1/ENCFF002AAV.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--------------------
51863 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

Num	12
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_21
Name	blacklist_filter peak 2
Thread	thread_Root
PID	51950

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

Start	2017-01-25 14:46:27
End	2017-01-25 14:47:34
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/rep2/ENCFF002AAW.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--------------------
51955 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

Num	13
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	57285

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

Start	2017-01-25 14:47:35
End	2017-01-25 14:47:44
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
57289 (process ID) old priority 0, new priority 10

Num	14
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	1123

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

Start	2017-01-25 14:47:45
End	2017-01-25 14:47:57
Elapsed	00:00:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.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/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/peak/macs2/overlap/ENCFF002AAV.nodup_ENCFF002AAW.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
1128 (process ID) old priority 0, new priority 10

Num	15
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	2010

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

Start	2017-01-25 14:47:58
End	2017-01-25 14:48:07
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/EncodeOtherHek293Data/H3K4me1/report/H3K4me1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/report/H3K4me1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/report/H3K4me1_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
2014 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/homer/default:/software/modulefiles/Matlab/MCR2010b:/software/modulefiles/align2rawsignal/2.0:/software/modulefiles/Matlab/R2014b
bool	allowEmpty	false
string[]	args	[-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep1/ENCFF002AAV.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1/align/rep2/ENCFF002AAW.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes, -no_pseudo_rep, -histone, -out_dir, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me1, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:13.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_wplrRU
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:homer/default:Matlab/MCR2010b:align2rawsignal/2.0:Matlab/R2014b
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/software/Matlab/R2014b/bin:/software/align2rawsignal/2.0/bin:/software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/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/EncodeOtherHek293Data/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/EncodeOtherHek293Data/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 42954 22
string	SSH_CONNECTION	171.65.77.8 42954 171.65.76.63 22
string	SSH_TTY	/dev/pts/152
string	STY	23838.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	XAPPLRESDIR	/software/Matlab/MCR2010b/v714/X11/app-defaults
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	22185
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope