Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170125_131646_271
Start time	2017-01-25 13:16:46
Run time	00:51:40.021
Tasks executed	15
Tasks failed	0
Tasks failed names
Arguments*	[-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.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/H3K4me3, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170125_131646_271/task.postalign_bed.pool_tag_pooled_rep.line_436.id_10 chipseq.bds.20170125_131646_271/task.postalign_bed.pool_tag_ppr1.line_436.id_11 chipseq.bds.20170125_131646_271/task.postalign_bed.pool_tag_ppr2.line_436.id_12 chipseq.bds.20170125_131646_271/task.callpeak_macs2.macs2_pooled_rep.line_71.id_13 chipseq.bds.20170125_131646_271/task.callpeak_macs2.macs2_ppr1.line_71.id_14 chipseq.bds.20170125_131646_271/task.callpeak_macs2.macs2_ppr2.line_71.id_15 chipseq.bds.20170125_131646_271/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16 chipseq.bds.20170125_131646_271/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17 chipseq.bds.20170125_131646_271/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_18 chipseq.bds.20170125_131646_271/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_19 chipseq.bds.20170125_131646_271/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_20 chipseq.bds.20170125_131646_271/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_21 chipseq.bds.20170125_131646_271/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170125_131646_271/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170125_131646_271/task.graphviz.report.line_97.id_24
thread_42	thread_Root
thread_43	thread_Root
thread_41	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	35508

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

Start	2017-01-25 13:16:51
End	2017-01-25 13:36:34
Elapsed	00:19:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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--------------------
20642 (process ID) old priority 0, new priority 10
Waiting for 13 seconds.

Num	2
ID	task.postalign_bed.pool_tag_ppr1.line_436.id_11
Name	pool_tag ppr1
Thread	thread_Root
PID	35509

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

Start	2017-01-25 13:16:52
End	2017-01-25 13:38:53
Elapsed	00:22:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pseudo_reps/rep1/pr1/ENCFF001FJZ.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pseudo_reps/rep2/pr1/ENCFF001FJY.nodup.pr1.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/align/pseudo_reps/rep1/pr1/ENCFF001FJZ.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pseudo_reps/rep2/pr1/ENCFF001FJY.nodup.pr1.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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--------------------
49514 (process ID) old priority 0, new priority 10

Num	3
ID	task.postalign_bed.pool_tag_ppr2.line_436.id_12
Name	pool_tag ppr2
Thread	thread_Root
PID	35510

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

Start	2017-01-25 13:16:53
End	2017-01-25 13:37:46
Elapsed	00:20:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pseudo_reps/rep1/pr2/ENCFF001FJZ.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pseudo_reps/rep2/pr2/ENCFF001FJY.nodup.pr2.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/align/pseudo_reps/rep1/pr2/ENCFF001FJZ.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pseudo_reps/rep2/pr2/ENCFF001FJY.nodup.pr2.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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--------------------
20787 (process ID) old priority 0, new priority 10
Waiting for 29 seconds.

Num	4
ID	task.callpeak_macs2.macs2_pooled_rep.line_71.id_13
Name	macs2 pooled_rep
Thread	thread_Root
PID	35511

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

Start	2017-01-25 13:38:55
End	2017-01-25 14:05:19
Elapsed	00:26:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep -o "ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep -o "ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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--------------------
11172 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 13:39:15: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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 13:39:15: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 13:39:15: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 13:39:16:  1000000 
INFO  @ Wed, 25 Jan 2017 13:39:18:  2000000 
INFO  @ Wed, 25 Jan 2017 13:39:20:  3000000 
INFO  @ Wed, 25 Jan 2017 13:39:21:  4000000 
INFO  @ Wed, 25 Jan 2017 13:39:23:  5000000 
INFO  @ Wed, 25 Jan 2017 13:39:24:  6000000 
INFO  @ Wed, 25 Jan 2017 13:39:26:  7000000 
INFO  @ Wed, 25 Jan 2017 13:39:28:  8000000 
INFO  @ Wed, 25 Jan 2017 13:39:29:  9000000 
INFO  @ Wed, 25 Jan 2017 13:39:31:  10000000 
INFO  @ Wed, 25 Jan 2017 13:39:32:  11000000 
INFO  @ Wed, 25 Jan 2017 13:39:34:  12000000 
INFO  @ Wed, 25 Jan 2017 13:39:35:  13000000 
INFO  @ Wed, 25 Jan 2017 13:39:37:  14000000 
INFO  @ Wed, 25 Jan 2017 13:39:38:  15000000 
INFO  @ Wed, 25 Jan 2017 13:39:40:  16000000 
INFO  @ Wed, 25 Jan 2017 13:39:42:  17000000 
INFO  @ Wed, 25 Jan 2017 13:39:43:  18000000 
INFO  @ Wed, 25 Jan 2017 13:39:46:  19000000 
INFO  @ Wed, 25 Jan 2017 13:39:48:  20000000 
INFO  @ Wed, 25 Jan 2017 13:39:49:  21000000 
INFO  @ Wed, 25 Jan 2017 13:39:51:  22000000 
INFO  @ Wed, 25 Jan 2017 13:39:52:  23000000 
INFO  @ Wed, 25 Jan 2017 13:39:54:  24000000 
INFO  @ Wed, 25 Jan 2017 13:39:55:  25000000 
INFO  @ Wed, 25 Jan 2017 13:39:57:  26000000 
INFO  @ Wed, 25 Jan 2017 13:39:58:  27000000 
INFO  @ Wed, 25 Jan 2017 13:40:00:  28000000 
INFO  @ Wed, 25 Jan 2017 13:40:01:  29000000 
INFO  @ Wed, 25 Jan 2017 13:40:03:  30000000 
INFO  @ Wed, 25 Jan 2017 13:40:04:  31000000 
INFO  @ Wed, 25 Jan 2017 13:40:06:  32000000 
INFO  @ Wed, 25 Jan 2017 13:40:07:  33000000 
INFO  @ Wed, 25 Jan 2017 13:40:09:  34000000 
INFO  @ Wed, 25 Jan 2017 13:40:11: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 13:40:13:  1000000 
INFO  @ Wed, 25 Jan 2017 13:40:15:  2000000 
INFO  @ Wed, 25 Jan 2017 13:40:16:  3000000 
INFO  @ Wed, 25 Jan 2017 13:40:18:  4000000 
INFO  @ Wed, 25 Jan 2017 13:40:19:  5000000 
INFO  @ Wed, 25 Jan 2017 13:40:21:  6000000 
INFO  @ Wed, 25 Jan 2017 13:40:22:  7000000 
INFO  @ Wed, 25 Jan 2017 13:40:24:  8000000 
INFO  @ Wed, 25 Jan 2017 13:40:25:  9000000 
INFO  @ Wed, 25 Jan 2017 13:40:27:  10000000 
INFO  @ Wed, 25 Jan 2017 13:40:28:  11000000 
INFO  @ Wed, 25 Jan 2017 13:40:29: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 13:40:29: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 13:40:29: #1  total tags in treatment: 34983396 
INFO  @ Wed, 25 Jan 2017 13:40:29: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 13:40:29: #1 finished! 
INFO  @ Wed, 25 Jan 2017 13:40:29: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 13:40:29: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 13:40:29: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 13:40:29: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 13:40:29: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 13:40:29: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 13:41:31: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 13:41:31: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 13:41:31: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 13:41:31: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 13:41:31: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 13:44:04: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 13:44:05: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 13:44:05: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 13:44:05: Done! 
INFO  @ Wed, 25 Jan 2017 13:44:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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 13:44:08: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 13:44:08: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 13:44:09:  1000000 
INFO  @ Wed, 25 Jan 2017 13:44:11:  2000000 
INFO  @ Wed, 25 Jan 2017 13:44:12:  3000000 
INFO  @ Wed, 25 Jan 2017 13:44:14:  4000000 
INFO  @ Wed, 25 Jan 2017 13:44:15:  5000000 
INFO  @ Wed, 25 Jan 2017 13:44:17:  6000000 
INFO  @ Wed, 25 Jan 2017 13:44:18:  7000000 
INFO  @ Wed, 25 Jan 2017 13:44:19:  8000000 
INFO  @ Wed, 25 Jan 2017 13:44:21:  9000000 
INFO  @ Wed, 25 Jan 2017 13:44:22:  10000000 
INFO  @ Wed, 25 Jan 2017 13:44:23:  11000000 
INFO  @ Wed, 25 Jan 2017 13:44:25:  12000000 
INFO  @ Wed, 25 Jan 2017 13:44:26:  13000000 
INFO  @ Wed, 25 Jan 2017 13:44:28:  14000000 
INFO  @ Wed, 25 Jan 2017 13:44:29:  15000000 
INFO  @ Wed, 25 Jan 2017 13:44:30:  16000000 
INFO  @ Wed, 25 Jan 2017 13:44:32:  17000000 
INFO  @ Wed, 25 Jan 2017 13:44:33:  18000000 
INFO  @ Wed, 25 Jan 2017 13:44:34:  19000000 
INFO  @ Wed, 25 Jan 2017 13:44:35:  20000000 
INFO  @ Wed, 25 Jan 2017 13:44:37:  21000000 
INFO  @ Wed, 25 Jan 2017 13:44:38:  22000000 
INFO  @ Wed, 25 Jan 2017 13:44:39:  23000000 
INFO  @ Wed, 25 Jan 2017 13:44:41:  24000000 
INFO  @ Wed, 25 Jan 2017 13:44:42:  25000000 
INFO  @ Wed, 25 Jan 2017 13:44:43:  26000000 
INFO  @ Wed, 25 Jan 2017 13:44:45:  27000000 
INFO  @ Wed, 25 Jan 2017 13:44:46:  28000000 
INFO  @ Wed, 25 Jan 2017 13:44:47:  29000000 
INFO  @ Wed, 25 Jan 2017 13:44:48:  30000000 
INFO  @ Wed, 25 Jan 2017 13:44:50:  31000000 
INFO  @ Wed, 25 Jan 2017 13:44:51:  32000000 
INFO  @ Wed, 25 Jan 2017 13:44:52:  33000000 
INFO  @ Wed, 25 Jan 2017 13:44:54:  34000000 
INFO  @ Wed, 25 Jan 2017 13:44:56: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 13:44:58:  1000000 
INFO  @ Wed, 25 Jan 2017 13:44:59:  2000000 
INFO  @ Wed, 25 Jan 2017 13:45:00:  3000000 
INFO  @ Wed, 25 Jan 2017 13:45:02:  4000000 
INFO  @ Wed, 25 Jan 2017 13:45:03:  5000000 
INFO  @ Wed, 25 Jan 2017 13:45:04:  6000000 
INFO  @ Wed, 25 Jan 2017 13:45:05:  7000000 
INFO  @ Wed, 25 Jan 2017 13:45:07:  8000000 
INFO  @ Wed, 25 Jan 2017 13:45:08:  9000000 
INFO  @ Wed, 25 Jan 2017 13:45:10:  10000000 
INFO  @ Wed, 25 Jan 2017 13:45:11:  11000000 
INFO  @ Wed, 25 Jan 2017 13:45:12: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 13:45:12: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 13:45:12: #1  total tags in treatment: 34983396 
INFO  @ Wed, 25 Jan 2017 13:45:12: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 13:45:12: #1 finished! 
INFO  @ Wed, 25 Jan 2017 13:45:12: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 13:45:12: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 13:45:12: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 13:45:12: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 13:45:12: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 13:45:12: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 13:46:03: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 13:47:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 13:47:05: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 13:47:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 13:47:05: Done! 
INFO  @ Wed, 25 Jan 2017 13:47:10: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 13:47:49: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 13:48:22: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 13:48:43: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 13:51:22: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 13:53:01: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 13:56:48: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 13:57:29: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 13:58:03: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 13:58:27: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 14:01:11: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 14:01:34: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 14:02:37: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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	35512

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

Start	2017-01-25 13:38:56
End	2017-01-25 13:46:03
Elapsed	00:07:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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--------------------
20977 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 13:39:12: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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 13:39:12: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 13:39:12: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 13:39:14:  1000000 
INFO  @ Wed, 25 Jan 2017 13:39:16:  2000000 
INFO  @ Wed, 25 Jan 2017 13:39:18:  3000000 
INFO  @ Wed, 25 Jan 2017 13:39:19:  4000000 
INFO  @ Wed, 25 Jan 2017 13:39:21:  5000000 
INFO  @ Wed, 25 Jan 2017 13:39:23:  6000000 
INFO  @ Wed, 25 Jan 2017 13:39:25:  7000000 
INFO  @ Wed, 25 Jan 2017 13:39:27:  8000000 
INFO  @ Wed, 25 Jan 2017 13:39:28:  9000000 
INFO  @ Wed, 25 Jan 2017 13:39:30:  10000000 
INFO  @ Wed, 25 Jan 2017 13:39:32:  11000000 
INFO  @ Wed, 25 Jan 2017 13:39:33:  12000000 
INFO  @ Wed, 25 Jan 2017 13:39:36:  13000000 
INFO  @ Wed, 25 Jan 2017 13:39:38:  14000000 
INFO  @ Wed, 25 Jan 2017 13:39:41:  15000000 
INFO  @ Wed, 25 Jan 2017 13:39:43:  16000000 
INFO  @ Wed, 25 Jan 2017 13:39:45:  17000000 
INFO  @ Wed, 25 Jan 2017 13:39:48: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 13:39:50:  1000000 
INFO  @ Wed, 25 Jan 2017 13:39:52:  2000000 
INFO  @ Wed, 25 Jan 2017 13:39:53:  3000000 
INFO  @ Wed, 25 Jan 2017 13:39:54:  4000000 
INFO  @ Wed, 25 Jan 2017 13:39:56:  5000000 
INFO  @ Wed, 25 Jan 2017 13:39:58:  6000000 
INFO  @ Wed, 25 Jan 2017 13:40:00:  7000000 
INFO  @ Wed, 25 Jan 2017 13:40:02:  8000000 
INFO  @ Wed, 25 Jan 2017 13:40:04:  9000000 
INFO  @ Wed, 25 Jan 2017 13:40:06:  10000000 
INFO  @ Wed, 25 Jan 2017 13:40:07:  11000000 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1 finished! 
INFO  @ Wed, 25 Jan 2017 13:40:08: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 13:40:08: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 13:41:12: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 13:41:12: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 13:41:12: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 13:41:12: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 13:41:12: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 13:43:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 13:43:21: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 13:43:22: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 13:43:22: Done! 
INFO  @ Wed, 25 Jan 2017 13:43:25: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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 13:43:25: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 13:43:25: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 13:43:26:  1000000 
INFO  @ Wed, 25 Jan 2017 13:43:28:  2000000 
INFO  @ Wed, 25 Jan 2017 13:43:30:  3000000 
INFO  @ Wed, 25 Jan 2017 13:43:31:  4000000 
INFO  @ Wed, 25 Jan 2017 13:43:33:  5000000 
INFO  @ Wed, 25 Jan 2017 13:43:34:  6000000 
INFO  @ Wed, 25 Jan 2017 13:43:36:  7000000 
INFO  @ Wed, 25 Jan 2017 13:43:37:  8000000 
INFO  @ Wed, 25 Jan 2017 13:43:39:  9000000 
INFO  @ Wed, 25 Jan 2017 13:43:40:  10000000 
INFO  @ Wed, 25 Jan 2017 13:43:42:  11000000 
INFO  @ Wed, 25 Jan 2017 13:43:44:  12000000 
INFO  @ Wed, 25 Jan 2017 13:43:45:  13000000 
INFO  @ Wed, 25 Jan 2017 13:43:47:  14000000 
INFO  @ Wed, 25 Jan 2017 13:43:48:  15000000 
INFO  @ Wed, 25 Jan 2017 13:43:50:  16000000 
INFO  @ Wed, 25 Jan 2017 13:43:51:  17000000 
INFO  @ Wed, 25 Jan 2017 13:43:53: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 13:43:55:  1000000 
INFO  @ Wed, 25 Jan 2017 13:43:57:  2000000 
INFO  @ Wed, 25 Jan 2017 13:43:58:  3000000 
INFO  @ Wed, 25 Jan 2017 13:43:59:  4000000 
INFO  @ Wed, 25 Jan 2017 13:44:01:  5000000 
INFO  @ Wed, 25 Jan 2017 13:44:02:  6000000 
INFO  @ Wed, 25 Jan 2017 13:44:04:  7000000 
INFO  @ Wed, 25 Jan 2017 13:44:05:  8000000 
INFO  @ Wed, 25 Jan 2017 13:44:07:  9000000 
INFO  @ Wed, 25 Jan 2017 13:44:08:  10000000 
INFO  @ Wed, 25 Jan 2017 13:44:10:  11000000 
INFO  @ Wed, 25 Jan 2017 13:44:11: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 13:44:11: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 13:44:11: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 13:44:11: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 13:44:11: #1 finished! 
INFO  @ Wed, 25 Jan 2017 13:44:11: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 13:44:11: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 13:44:11: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 13:44:11: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 13:44:11: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 13:44:11: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 13:45:04: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 13:45:57: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 13:45:58: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 13:45:58: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 13:45:59: Done!

Num	6
ID	task.callpeak_macs2.macs2_ppr2.line_71.id_15
Name	macs2 ppr2
Thread	thread_Root
PID	35513

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

Start	2017-01-25 13:38:57
End	2017-01-25 13:46:05
Elapsed	00:07:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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--------------------
20976 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 13:39:12: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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 13:39:12: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 13:39:12: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 13:39:14:  1000000 
INFO  @ Wed, 25 Jan 2017 13:39:16:  2000000 
INFO  @ Wed, 25 Jan 2017 13:39:18:  3000000 
INFO  @ Wed, 25 Jan 2017 13:39:19:  4000000 
INFO  @ Wed, 25 Jan 2017 13:39:21:  5000000 
INFO  @ Wed, 25 Jan 2017 13:39:23:  6000000 
INFO  @ Wed, 25 Jan 2017 13:39:25:  7000000 
INFO  @ Wed, 25 Jan 2017 13:39:27:  8000000 
INFO  @ Wed, 25 Jan 2017 13:39:29:  9000000 
INFO  @ Wed, 25 Jan 2017 13:39:30:  10000000 
INFO  @ Wed, 25 Jan 2017 13:39:32:  11000000 
INFO  @ Wed, 25 Jan 2017 13:39:34:  12000000 
INFO  @ Wed, 25 Jan 2017 13:39:36:  13000000 
INFO  @ Wed, 25 Jan 2017 13:39:38:  14000000 
INFO  @ Wed, 25 Jan 2017 13:39:40:  15000000 
INFO  @ Wed, 25 Jan 2017 13:39:42:  16000000 
INFO  @ Wed, 25 Jan 2017 13:39:44:  17000000 
INFO  @ Wed, 25 Jan 2017 13:39:47: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 13:39:49:  1000000 
INFO  @ Wed, 25 Jan 2017 13:39:51:  2000000 
INFO  @ Wed, 25 Jan 2017 13:39:53:  3000000 
INFO  @ Wed, 25 Jan 2017 13:39:54:  4000000 
INFO  @ Wed, 25 Jan 2017 13:39:56:  5000000 
INFO  @ Wed, 25 Jan 2017 13:39:58:  6000000 
INFO  @ Wed, 25 Jan 2017 13:39:59:  7000000 
INFO  @ Wed, 25 Jan 2017 13:40:01:  8000000 
INFO  @ Wed, 25 Jan 2017 13:40:03:  9000000 
INFO  @ Wed, 25 Jan 2017 13:40:05:  10000000 
INFO  @ Wed, 25 Jan 2017 13:40:07:  11000000 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 13:40:08: #1 finished! 
INFO  @ Wed, 25 Jan 2017 13:40:08: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 13:40:08: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 13:40:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 13:41:07: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 13:41:07: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 13:41:07: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 13:41:07: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 13:41:07: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 13:43:12: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 13:43:12: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 13:43:12: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 13:43:13: Done! 
INFO  @ Wed, 25 Jan 2017 13:43:15: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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 13:43:15: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 13:43:15: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 13:43:18:  1000000 
INFO  @ Wed, 25 Jan 2017 13:43:20:  2000000 
INFO  @ Wed, 25 Jan 2017 13:43:22:  3000000 
INFO  @ Wed, 25 Jan 2017 13:43:23:  4000000 
INFO  @ Wed, 25 Jan 2017 13:43:25:  5000000 
INFO  @ Wed, 25 Jan 2017 13:43:27:  6000000 
INFO  @ Wed, 25 Jan 2017 13:43:29:  7000000 
INFO  @ Wed, 25 Jan 2017 13:43:31:  8000000 
INFO  @ Wed, 25 Jan 2017 13:43:32:  9000000 
INFO  @ Wed, 25 Jan 2017 13:43:34:  10000000 
INFO  @ Wed, 25 Jan 2017 13:43:36:  11000000 
INFO  @ Wed, 25 Jan 2017 13:43:37:  12000000 
INFO  @ Wed, 25 Jan 2017 13:43:39:  13000000 
INFO  @ Wed, 25 Jan 2017 13:43:41:  14000000 
INFO  @ Wed, 25 Jan 2017 13:43:42:  15000000 
INFO  @ Wed, 25 Jan 2017 13:43:44:  16000000 
INFO  @ Wed, 25 Jan 2017 13:43:46:  17000000 
INFO  @ Wed, 25 Jan 2017 13:43:47: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 13:43:49:  1000000 
INFO  @ Wed, 25 Jan 2017 13:43:51:  2000000 
INFO  @ Wed, 25 Jan 2017 13:43:52:  3000000 
INFO  @ Wed, 25 Jan 2017 13:43:54:  4000000 
INFO  @ Wed, 25 Jan 2017 13:43:55:  5000000 
INFO  @ Wed, 25 Jan 2017 13:43:57:  6000000 
INFO  @ Wed, 25 Jan 2017 13:43:58:  7000000 
INFO  @ Wed, 25 Jan 2017 13:44:00:  8000000 
INFO  @ Wed, 25 Jan 2017 13:44:01:  9000000 
INFO  @ Wed, 25 Jan 2017 13:44:03:  10000000 
INFO  @ Wed, 25 Jan 2017 13:44:05:  11000000 
INFO  @ Wed, 25 Jan 2017 13:44:05: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 13:44:05: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 13:44:05: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 13:44:05: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 13:44:05: #1 finished! 
INFO  @ Wed, 25 Jan 2017 13:44:05: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 13:44:05: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 13:44:05: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 13:44:05: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 13:44:05: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 13:44:05: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 13:45:07: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 13:45:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 13:46:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 13:46:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 13:46:01: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	35515

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

Start	2017-01-25 14:05:20
End	2017-01-25 14:06:38
Elapsed	00:01:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.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/H3K4me3/peak/macs2/rep2/ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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--------------------
22715 (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	35516

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

Start	2017-01-25 14:05:21
End	2017-01-25 14:06:39
Elapsed	00:01:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.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/H3K4me3/peak/macs2/rep2/ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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--------------------
22713 (process ID) old priority 0, new priority 10
Waiting for 54 seconds.

Num	9
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_18
Name	naive_overlap_thresh
Thread	thread_Root
PID	35517

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

Start	2017-01-25 14:05:22
End	2017-01-25 14:06:39
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.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/H3K4me3/peak/macs2/rep2/ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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--------------------
22714 (process ID) old priority 0, new priority 10
Waiting for 55 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	15755

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

Start	2017-01-25 14:06:41
End	2017-01-25 14:07:55
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.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--------------------
15759 (process ID) old priority 0, new priority 10
Waiting for 59 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	15882

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

Start	2017-01-25 14:06:42
End	2017-01-25 14:07:55
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.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/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.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/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.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--------------------
15887 (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	15938

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

Start	2017-01-25 14:06:43
End	2017-01-25 14:07:55
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.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/H3K4me3/peak/macs2/rep2/ENCFF001FJY.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/H3K4me3/peak/macs2/rep2/ENCFF001FJY.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--------------------
15944 (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	20932

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

Start	2017-01-25 14:07:56
End	2017-01-25 14:08:05
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
20936 (process ID) old priority 0, new priority 10

Num	14
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	21571

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

Start	2017-01-25 14:08:06
End	2017-01-25 14:08:15
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.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/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
21575 (process ID) old priority 0, new priority 10

Num	15
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	22177

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

Start	2017-01-25 14:08:17
End	2017-01-25 14:08:26
Elapsed	00:00:09
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/H3K4me3/report/H3K4me3_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/report/H3K4me3_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/report/H3K4me3_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
22181 (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/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.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/H3K4me3, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:13.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_wplrRU
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:homer/default:Matlab/MCR2010b:align2rawsignal/2.0:Matlab/R2014b
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/H3K4me3
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/H3K4me3
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	3195.H3K4me3.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