Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170413_131502_349
Start time	2017-04-13 13:15:02
Run time	02:56:14.108
Tasks executed	34
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZIC2_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZIC2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17 chipseq.bds.20170413_131502_349/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18 chipseq.bds.20170413_131502_349/task.callpeak_naive_overlap.naive_overlap.line_143.id_19 chipseq.bds.20170413_131502_349/task.callpeak_idr.idr2_rep1_rep2.line_74.id_20 chipseq.bds.20170413_131502_349/task.callpeak_idr.idr2_rep1_pr.line_74.id_21 chipseq.bds.20170413_131502_349/task.callpeak_idr.idr2_rep2_pr.line_74.id_22 chipseq.bds.20170413_131502_349/task.callpeak_idr.idr2_ppr.line_74.id_23 chipseq.bds.20170413_131502_349/task.sys.copy_file.line_131.id_32 chipseq.bds.20170413_131502_349/task.sys.copy_file.line_131.id_33 chipseq.bds.20170413_131502_349/task.sys.copy_file.line_131.id_34 chipseq.bds.20170413_131502_349/task.sys.copy_file.line_131.id_35 chipseq.bds.20170413_131502_349/task.callpeak_idr.idr_final_qc.line_283.id_36 chipseq.bds.20170413_131502_349/task.callpeak_idr.FRiP_rep1_pr.line_120.id_37 chipseq.bds.20170413_131502_349/task.callpeak_idr.FRiP_rep2_pr.line_120.id_38 chipseq.bds.20170413_131502_349/task.callpeak_idr.FRiP_ppr.line_120.id_39 chipseq.bds.20170413_131502_349/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_40 chipseq.bds.20170413_131502_349/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_41 chipseq.bds.20170413_131502_349/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_42 chipseq.bds.20170413_131502_349/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_43 chipseq.bds.20170413_131502_349/task.report.peak2hammock.line_361.id_46 chipseq.bds.20170413_131502_349/task.report.peak2hammock.line_361.id_47 chipseq.bds.20170413_131502_349/task.report.peak2hammock.line_361.id_48 chipseq.bds.20170413_131502_349/task.report.peak2hammock.line_361.id_49 chipseq.bds.20170413_131502_349/task.report.peak2hammock.line_361.id_50 chipseq.bds.20170413_131502_349/task.graphviz.report.line_97.id_51 chipseq.bds.20170413_131502_349/task.report.pdf2png.line_328.id_52 chipseq.bds.20170413_131502_349/task.report.pdf2png.line_328.id_53
thread_41	thread_Root
thread_42	thread_Root
thread_43	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10
Name	macs2 n/s pooled_rep
Thread	thread_Root
PID	46802

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

Start	2017-04-13 13:15:15
End	2017-04-13 15:54:57
Elapsed	02:39:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
12306 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:15:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:15:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:15:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:15:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:15:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:15:40:  3000000 
INFO  @ Thu, 13 Apr 2017 13:15:42:  4000000 
INFO  @ Thu, 13 Apr 2017 13:15:44:  5000000 
INFO  @ Thu, 13 Apr 2017 13:15:45:  6000000 
INFO  @ Thu, 13 Apr 2017 13:15:47:  7000000 
INFO  @ Thu, 13 Apr 2017 13:15:49:  8000000 
INFO  @ Thu, 13 Apr 2017 13:15:51:  9000000 
INFO  @ Thu, 13 Apr 2017 13:15:53:  10000000 
INFO  @ Thu, 13 Apr 2017 13:15:55:  11000000 
INFO  @ Thu, 13 Apr 2017 13:15:57:  12000000 
INFO  @ Thu, 13 Apr 2017 13:15:59:  13000000 
INFO  @ Thu, 13 Apr 2017 13:16:01:  14000000 
INFO  @ Thu, 13 Apr 2017 13:16:03:  15000000 
INFO  @ Thu, 13 Apr 2017 13:16:05:  16000000 
INFO  @ Thu, 13 Apr 2017 13:16:07:  17000000 
INFO  @ Thu, 13 Apr 2017 13:16:09:  18000000 
INFO  @ Thu, 13 Apr 2017 13:16:11:  19000000 
INFO  @ Thu, 13 Apr 2017 13:16:13:  20000000 
INFO  @ Thu, 13 Apr 2017 13:16:15:  21000000 
INFO  @ Thu, 13 Apr 2017 13:16:17:  22000000 
INFO  @ Thu, 13 Apr 2017 13:16:19:  23000000 
INFO  @ Thu, 13 Apr 2017 13:16:21:  24000000 
INFO  @ Thu, 13 Apr 2017 13:16:23:  25000000 
INFO  @ Thu, 13 Apr 2017 13:16:25:  26000000 
INFO  @ Thu, 13 Apr 2017 13:16:27:  27000000 
INFO  @ Thu, 13 Apr 2017 13:16:29:  28000000 
INFO  @ Thu, 13 Apr 2017 13:16:31:  29000000 
INFO  @ Thu, 13 Apr 2017 13:16:33:  30000000 
INFO  @ Thu, 13 Apr 2017 13:16:35:  31000000 
INFO  @ Thu, 13 Apr 2017 13:16:37:  32000000 
INFO  @ Thu, 13 Apr 2017 13:16:39:  33000000 
INFO  @ Thu, 13 Apr 2017 13:16:41:  34000000 
INFO  @ Thu, 13 Apr 2017 13:16:43:  35000000 
INFO  @ Thu, 13 Apr 2017 13:16:45:  36000000 
INFO  @ Thu, 13 Apr 2017 13:16:47:  37000000 
INFO  @ Thu, 13 Apr 2017 13:16:49:  38000000 
INFO  @ Thu, 13 Apr 2017 13:16:51:  39000000 
INFO  @ Thu, 13 Apr 2017 13:16:52:  40000000 
INFO  @ Thu, 13 Apr 2017 13:16:54:  41000000 
INFO  @ Thu, 13 Apr 2017 13:16:56:  42000000 
INFO  @ Thu, 13 Apr 2017 13:16:58:  43000000 
INFO  @ Thu, 13 Apr 2017 13:17:00:  44000000 
INFO  @ Thu, 13 Apr 2017 13:17:02:  45000000 
INFO  @ Thu, 13 Apr 2017 13:17:04:  46000000 
INFO  @ Thu, 13 Apr 2017 13:17:06:  47000000 
INFO  @ Thu, 13 Apr 2017 13:17:08:  48000000 
INFO  @ Thu, 13 Apr 2017 13:17:10:  49000000 
INFO  @ Thu, 13 Apr 2017 13:17:12:  50000000 
INFO  @ Thu, 13 Apr 2017 13:17:14:  51000000 
INFO  @ Thu, 13 Apr 2017 13:17:16:  52000000 
INFO  @ Thu, 13 Apr 2017 13:17:18:  53000000 
INFO  @ Thu, 13 Apr 2017 13:17:20:  54000000 
INFO  @ Thu, 13 Apr 2017 13:17:22:  55000000 
INFO  @ Thu, 13 Apr 2017 13:17:24:  56000000 
INFO  @ Thu, 13 Apr 2017 13:17:26:  57000000 
INFO  @ Thu, 13 Apr 2017 13:17:28:  58000000 
INFO  @ Thu, 13 Apr 2017 13:17:30:  59000000 
INFO  @ Thu, 13 Apr 2017 13:17:32:  60000000 
INFO  @ Thu, 13 Apr 2017 13:17:34:  61000000 
INFO  @ Thu, 13 Apr 2017 13:17:36:  62000000 
INFO  @ Thu, 13 Apr 2017 13:17:38:  63000000 
INFO  @ Thu, 13 Apr 2017 13:17:40:  64000000 
INFO  @ Thu, 13 Apr 2017 13:17:42:  65000000 
INFO  @ Thu, 13 Apr 2017 13:17:44:  66000000 
INFO  @ Thu, 13 Apr 2017 13:17:46:  67000000 
INFO  @ Thu, 13 Apr 2017 13:17:48:  68000000 
INFO  @ Thu, 13 Apr 2017 13:17:50:  69000000 
INFO  @ Thu, 13 Apr 2017 13:17:52:  70000000 
INFO  @ Thu, 13 Apr 2017 13:17:54:  71000000 
INFO  @ Thu, 13 Apr 2017 13:17:56:  72000000 
INFO  @ Thu, 13 Apr 2017 13:17:58:  73000000 
INFO  @ Thu, 13 Apr 2017 13:18:00:  74000000 
INFO  @ Thu, 13 Apr 2017 13:18:02:  75000000 
INFO  @ Thu, 13 Apr 2017 13:18:04:  76000000 
INFO  @ Thu, 13 Apr 2017 13:18:06:  77000000 
INFO  @ Thu, 13 Apr 2017 13:18:08:  78000000 
INFO  @ Thu, 13 Apr 2017 13:18:09:  79000000 
INFO  @ Thu, 13 Apr 2017 13:18:11:  80000000 
INFO  @ Thu, 13 Apr 2017 13:18:13:  81000000 
INFO  @ Thu, 13 Apr 2017 13:18:15:  82000000 
INFO  @ Thu, 13 Apr 2017 13:18:17:  83000000 
INFO  @ Thu, 13 Apr 2017 13:18:19:  84000000 
INFO  @ Thu, 13 Apr 2017 13:18:21:  85000000 
INFO  @ Thu, 13 Apr 2017 13:18:23:  86000000 
INFO  @ Thu, 13 Apr 2017 13:18:25:  87000000 
INFO  @ Thu, 13 Apr 2017 13:18:27:  88000000 
INFO  @ Thu, 13 Apr 2017 13:18:29:  89000000 
INFO  @ Thu, 13 Apr 2017 13:18:31:  90000000 
INFO  @ Thu, 13 Apr 2017 13:18:33:  91000000 
INFO  @ Thu, 13 Apr 2017 13:18:35:  92000000 
INFO  @ Thu, 13 Apr 2017 13:18:37:  93000000 
INFO  @ Thu, 13 Apr 2017 13:18:39:  94000000 
INFO  @ Thu, 13 Apr 2017 13:18:41:  95000000 
INFO  @ Thu, 13 Apr 2017 13:18:43:  96000000 
INFO  @ Thu, 13 Apr 2017 13:18:45:  97000000 
INFO  @ Thu, 13 Apr 2017 13:18:47:  98000000 
INFO  @ Thu, 13 Apr 2017 13:18:49:  99000000 
INFO  @ Thu, 13 Apr 2017 13:18:51:  100000000 
INFO  @ Thu, 13 Apr 2017 13:18:53:  101000000 
INFO  @ Thu, 13 Apr 2017 13:18:55:  102000000 
INFO  @ Thu, 13 Apr 2017 13:18:57:  103000000 
INFO  @ Thu, 13 Apr 2017 13:18:59:  104000000 
INFO  @ Thu, 13 Apr 2017 13:19:01:  105000000 
INFO  @ Thu, 13 Apr 2017 13:19:03:  106000000 
INFO  @ Thu, 13 Apr 2017 13:19:05:  107000000 
INFO  @ Thu, 13 Apr 2017 13:19:07:  108000000 
INFO  @ Thu, 13 Apr 2017 13:19:17: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:19:19:  1000000 
INFO  @ Thu, 13 Apr 2017 13:19:21:  2000000 
INFO  @ Thu, 13 Apr 2017 13:19:23:  3000000 
INFO  @ Thu, 13 Apr 2017 13:19:25:  4000000 
INFO  @ Thu, 13 Apr 2017 13:19:26:  5000000 
INFO  @ Thu, 13 Apr 2017 13:19:28:  6000000 
INFO  @ Thu, 13 Apr 2017 13:19:30:  7000000 
INFO  @ Thu, 13 Apr 2017 13:19:32:  8000000 
INFO  @ Thu, 13 Apr 2017 13:19:34:  9000000 
INFO  @ Thu, 13 Apr 2017 13:19:36:  10000000 
INFO  @ Thu, 13 Apr 2017 13:19:37:  11000000 
INFO  @ Thu, 13 Apr 2017 13:19:39:  12000000 
INFO  @ Thu, 13 Apr 2017 13:19:41:  13000000 
INFO  @ Thu, 13 Apr 2017 13:19:43:  14000000 
INFO  @ Thu, 13 Apr 2017 13:19:45:  15000000 
INFO  @ Thu, 13 Apr 2017 13:19:47:  16000000 
INFO  @ Thu, 13 Apr 2017 13:19:49:  17000000 
INFO  @ Thu, 13 Apr 2017 13:19:50:  18000000 
INFO  @ Thu, 13 Apr 2017 13:19:52:  19000000 
INFO  @ Thu, 13 Apr 2017 13:19:54:  20000000 
INFO  @ Thu, 13 Apr 2017 13:19:56:  21000000 
INFO  @ Thu, 13 Apr 2017 13:19:58:  22000000 
INFO  @ Thu, 13 Apr 2017 13:20:00:  23000000 
INFO  @ Thu, 13 Apr 2017 13:20:01:  24000000 
INFO  @ Thu, 13 Apr 2017 13:20:03:  25000000 
INFO  @ Thu, 13 Apr 2017 13:20:05:  26000000 
INFO  @ Thu, 13 Apr 2017 13:20:07:  27000000 
INFO  @ Thu, 13 Apr 2017 13:20:09:  28000000 
INFO  @ Thu, 13 Apr 2017 13:20:11:  29000000 
INFO  @ Thu, 13 Apr 2017 13:20:13:  30000000 
INFO  @ Thu, 13 Apr 2017 13:20:14:  31000000 
INFO  @ Thu, 13 Apr 2017 13:20:16:  32000000 
INFO  @ Thu, 13 Apr 2017 13:20:18:  33000000 
INFO  @ Thu, 13 Apr 2017 13:20:20:  34000000 
INFO  @ Thu, 13 Apr 2017 13:20:22:  35000000 
INFO  @ Thu, 13 Apr 2017 13:20:24:  36000000 
INFO  @ Thu, 13 Apr 2017 13:20:25:  37000000 
INFO  @ Thu, 13 Apr 2017 13:20:27:  38000000 
INFO  @ Thu, 13 Apr 2017 13:20:29:  39000000 
INFO  @ Thu, 13 Apr 2017 13:20:31:  40000000 
INFO  @ Thu, 13 Apr 2017 13:20:33:  41000000 
INFO  @ Thu, 13 Apr 2017 13:20:35:  42000000 
INFO  @ Thu, 13 Apr 2017 13:20:36:  43000000 
INFO  @ Thu, 13 Apr 2017 13:20:38:  44000000 
INFO  @ Thu, 13 Apr 2017 13:20:40:  45000000 
INFO  @ Thu, 13 Apr 2017 13:20:42:  46000000 
INFO  @ Thu, 13 Apr 2017 13:20:44:  47000000 
INFO  @ Thu, 13 Apr 2017 13:20:46:  48000000 
INFO  @ Thu, 13 Apr 2017 13:20:47:  49000000 
INFO  @ Thu, 13 Apr 2017 13:20:49:  50000000 
INFO  @ Thu, 13 Apr 2017 13:20:51:  51000000 
INFO  @ Thu, 13 Apr 2017 13:20:53:  52000000 
INFO  @ Thu, 13 Apr 2017 13:20:55:  53000000 
INFO  @ Thu, 13 Apr 2017 13:20:57:  54000000 
INFO  @ Thu, 13 Apr 2017 13:20:58:  55000000 
INFO  @ Thu, 13 Apr 2017 13:21:00:  56000000 
INFO  @ Thu, 13 Apr 2017 13:21:02:  57000000 
INFO  @ Thu, 13 Apr 2017 13:21:04:  58000000 
INFO  @ Thu, 13 Apr 2017 13:21:06:  59000000 
INFO  @ Thu, 13 Apr 2017 13:21:08:  60000000 
INFO  @ Thu, 13 Apr 2017 13:21:10:  61000000 
INFO  @ Thu, 13 Apr 2017 13:21:11:  62000000 
INFO  @ Thu, 13 Apr 2017 13:21:13:  63000000 
INFO  @ Thu, 13 Apr 2017 13:21:15:  64000000 
INFO  @ Thu, 13 Apr 2017 13:21:17:  65000000 
INFO  @ Thu, 13 Apr 2017 13:21:19:  66000000 
INFO  @ Thu, 13 Apr 2017 13:21:21:  67000000 
INFO  @ Thu, 13 Apr 2017 13:21:23:  68000000 
INFO  @ Thu, 13 Apr 2017 13:21:24:  69000000 
INFO  @ Thu, 13 Apr 2017 13:21:26:  70000000 
INFO  @ Thu, 13 Apr 2017 13:21:28:  71000000 
INFO  @ Thu, 13 Apr 2017 13:21:30:  72000000 
INFO  @ Thu, 13 Apr 2017 13:21:32:  73000000 
INFO  @ Thu, 13 Apr 2017 13:21:34:  74000000 
INFO  @ Thu, 13 Apr 2017 13:21:35:  75000000 
INFO  @ Thu, 13 Apr 2017 13:21:37:  76000000 
INFO  @ Thu, 13 Apr 2017 13:21:39:  77000000 
INFO  @ Thu, 13 Apr 2017 13:21:41:  78000000 
INFO  @ Thu, 13 Apr 2017 13:21:43:  79000000 
INFO  @ Thu, 13 Apr 2017 13:21:45:  80000000 
INFO  @ Thu, 13 Apr 2017 13:21:46:  81000000 
INFO  @ Thu, 13 Apr 2017 13:21:48:  82000000 
INFO  @ Thu, 13 Apr 2017 13:21:50:  83000000 
INFO  @ Thu, 13 Apr 2017 13:21:52:  84000000 
INFO  @ Thu, 13 Apr 2017 13:21:54:  85000000 
INFO  @ Thu, 13 Apr 2017 13:21:56:  86000000 
INFO  @ Thu, 13 Apr 2017 13:21:57:  87000000 
INFO  @ Thu, 13 Apr 2017 13:21:59:  88000000 
INFO  @ Thu, 13 Apr 2017 13:22:01:  89000000 
INFO  @ Thu, 13 Apr 2017 13:22:03:  90000000 
INFO  @ Thu, 13 Apr 2017 13:22:05:  91000000 
INFO  @ Thu, 13 Apr 2017 13:22:07:  92000000 
INFO  @ Thu, 13 Apr 2017 13:22:09:  93000000 
INFO  @ Thu, 13 Apr 2017 13:22:10:  94000000 
INFO  @ Thu, 13 Apr 2017 13:22:12:  95000000 
INFO  @ Thu, 13 Apr 2017 13:22:14:  96000000 
INFO  @ Thu, 13 Apr 2017 13:22:16:  97000000 
INFO  @ Thu, 13 Apr 2017 13:22:18:  98000000 
INFO  @ Thu, 13 Apr 2017 13:22:19:  99000000 
INFO  @ Thu, 13 Apr 2017 13:22:21: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:22:21: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:22:21: #1  total tags in treatment: 108422852 
INFO  @ Thu, 13 Apr 2017 13:22:21: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:22:21: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:22:21: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:22:21: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:22:21: #2 Use 213 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:22:21: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:22:21: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:22:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:30:32: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:30:32: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:30:32: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:30:32: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:30:32: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:45:52: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:45:54: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:45:55: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:45:56: Done! 
INFO  @ Thu, 13 Apr 2017 13:45:59: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:49:57: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:53:19: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 13:56:15: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:12:28: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:24:43: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:52:08: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:56:03: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:59:26: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 15:01:48: Values in your input bedGraph files will be multiplied by 99.493262 ... 
INFO  @ Thu, 13 Apr 2017 15:17:31: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 15:21:21: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:30:34: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'!

Num	2
ID	task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11
Name	macs2 n/s ppr1
Thread	thread_Root
PID	46803

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

Start	2017-04-13 13:15:15
End	2017-04-13 13:35:33
Elapsed	00:20:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
46206 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:15:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:15:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:15:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:15:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:15:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:15:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:15:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:15:42:  5000000 
INFO  @ Thu, 13 Apr 2017 13:15:44:  6000000 
INFO  @ Thu, 13 Apr 2017 13:15:45:  7000000 
INFO  @ Thu, 13 Apr 2017 13:15:47:  8000000 
INFO  @ Thu, 13 Apr 2017 13:15:48:  9000000 
INFO  @ Thu, 13 Apr 2017 13:15:50:  10000000 
INFO  @ Thu, 13 Apr 2017 13:15:51:  11000000 
INFO  @ Thu, 13 Apr 2017 13:15:53:  12000000 
INFO  @ Thu, 13 Apr 2017 13:15:54:  13000000 
INFO  @ Thu, 13 Apr 2017 13:15:56:  14000000 
INFO  @ Thu, 13 Apr 2017 13:15:57:  15000000 
INFO  @ Thu, 13 Apr 2017 13:15:59:  16000000 
INFO  @ Thu, 13 Apr 2017 13:16:00:  17000000 
INFO  @ Thu, 13 Apr 2017 13:16:02:  18000000 
INFO  @ Thu, 13 Apr 2017 13:16:03:  19000000 
INFO  @ Thu, 13 Apr 2017 13:16:05:  20000000 
INFO  @ Thu, 13 Apr 2017 13:16:06:  21000000 
INFO  @ Thu, 13 Apr 2017 13:16:08:  22000000 
INFO  @ Thu, 13 Apr 2017 13:16:09:  23000000 
INFO  @ Thu, 13 Apr 2017 13:16:11:  24000000 
INFO  @ Thu, 13 Apr 2017 13:16:12:  25000000 
INFO  @ Thu, 13 Apr 2017 13:16:14:  26000000 
INFO  @ Thu, 13 Apr 2017 13:16:15:  27000000 
INFO  @ Thu, 13 Apr 2017 13:16:17:  28000000 
INFO  @ Thu, 13 Apr 2017 13:16:19:  29000000 
INFO  @ Thu, 13 Apr 2017 13:16:20:  30000000 
INFO  @ Thu, 13 Apr 2017 13:16:22:  31000000 
INFO  @ Thu, 13 Apr 2017 13:16:23:  32000000 
INFO  @ Thu, 13 Apr 2017 13:16:25:  33000000 
INFO  @ Thu, 13 Apr 2017 13:16:26:  34000000 
INFO  @ Thu, 13 Apr 2017 13:16:28:  35000000 
INFO  @ Thu, 13 Apr 2017 13:16:29:  36000000 
INFO  @ Thu, 13 Apr 2017 13:16:31:  37000000 
INFO  @ Thu, 13 Apr 2017 13:16:32:  38000000 
INFO  @ Thu, 13 Apr 2017 13:16:34:  39000000 
INFO  @ Thu, 13 Apr 2017 13:16:35:  40000000 
INFO  @ Thu, 13 Apr 2017 13:16:37:  41000000 
INFO  @ Thu, 13 Apr 2017 13:16:38:  42000000 
INFO  @ Thu, 13 Apr 2017 13:16:40:  43000000 
INFO  @ Thu, 13 Apr 2017 13:16:41:  44000000 
INFO  @ Thu, 13 Apr 2017 13:16:42:  45000000 
INFO  @ Thu, 13 Apr 2017 13:16:44:  46000000 
INFO  @ Thu, 13 Apr 2017 13:16:45:  47000000 
INFO  @ Thu, 13 Apr 2017 13:16:47:  48000000 
INFO  @ Thu, 13 Apr 2017 13:16:48:  49000000 
INFO  @ Thu, 13 Apr 2017 13:16:50:  50000000 
INFO  @ Thu, 13 Apr 2017 13:16:52:  51000000 
INFO  @ Thu, 13 Apr 2017 13:16:53:  52000000 
INFO  @ Thu, 13 Apr 2017 13:16:55:  53000000 
INFO  @ Thu, 13 Apr 2017 13:16:56:  54000000 
INFO  @ Thu, 13 Apr 2017 13:17:00: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:17:01:  1000000 
INFO  @ Thu, 13 Apr 2017 13:17:03:  2000000 
INFO  @ Thu, 13 Apr 2017 13:17:04:  3000000 
INFO  @ Thu, 13 Apr 2017 13:17:05:  4000000 
INFO  @ Thu, 13 Apr 2017 13:17:07:  5000000 
INFO  @ Thu, 13 Apr 2017 13:17:08:  6000000 
INFO  @ Thu, 13 Apr 2017 13:17:09:  7000000 
INFO  @ Thu, 13 Apr 2017 13:17:11:  8000000 
INFO  @ Thu, 13 Apr 2017 13:17:12:  9000000 
INFO  @ Thu, 13 Apr 2017 13:17:14:  10000000 
INFO  @ Thu, 13 Apr 2017 13:17:15:  11000000 
INFO  @ Thu, 13 Apr 2017 13:17:16:  12000000 
INFO  @ Thu, 13 Apr 2017 13:17:18:  13000000 
INFO  @ Thu, 13 Apr 2017 13:17:19:  14000000 
INFO  @ Thu, 13 Apr 2017 13:17:21:  15000000 
INFO  @ Thu, 13 Apr 2017 13:17:22:  16000000 
INFO  @ Thu, 13 Apr 2017 13:17:23:  17000000 
INFO  @ Thu, 13 Apr 2017 13:17:25:  18000000 
INFO  @ Thu, 13 Apr 2017 13:17:26:  19000000 
INFO  @ Thu, 13 Apr 2017 13:17:28:  20000000 
INFO  @ Thu, 13 Apr 2017 13:17:29:  21000000 
INFO  @ Thu, 13 Apr 2017 13:17:31:  22000000 
INFO  @ Thu, 13 Apr 2017 13:17:32:  23000000 
INFO  @ Thu, 13 Apr 2017 13:17:33:  24000000 
INFO  @ Thu, 13 Apr 2017 13:17:35:  25000000 
INFO  @ Thu, 13 Apr 2017 13:17:36:  26000000 
INFO  @ Thu, 13 Apr 2017 13:17:38:  27000000 
INFO  @ Thu, 13 Apr 2017 13:17:39:  28000000 
INFO  @ Thu, 13 Apr 2017 13:17:41:  29000000 
INFO  @ Thu, 13 Apr 2017 13:17:42:  30000000 
INFO  @ Thu, 13 Apr 2017 13:17:43:  31000000 
INFO  @ Thu, 13 Apr 2017 13:17:45:  32000000 
INFO  @ Thu, 13 Apr 2017 13:17:47:  33000000 
INFO  @ Thu, 13 Apr 2017 13:17:48:  34000000 
INFO  @ Thu, 13 Apr 2017 13:17:50:  35000000 
INFO  @ Thu, 13 Apr 2017 13:17:51:  36000000 
INFO  @ Thu, 13 Apr 2017 13:17:53:  37000000 
INFO  @ Thu, 13 Apr 2017 13:17:54:  38000000 
INFO  @ Thu, 13 Apr 2017 13:17:55:  39000000 
INFO  @ Thu, 13 Apr 2017 13:17:57:  40000000 
INFO  @ Thu, 13 Apr 2017 13:17:58:  41000000 
INFO  @ Thu, 13 Apr 2017 13:17:59:  42000000 
INFO  @ Thu, 13 Apr 2017 13:18:01:  43000000 
INFO  @ Thu, 13 Apr 2017 13:18:02:  44000000 
INFO  @ Thu, 13 Apr 2017 13:18:04:  45000000 
INFO  @ Thu, 13 Apr 2017 13:18:05:  46000000 
INFO  @ Thu, 13 Apr 2017 13:18:06:  47000000 
INFO  @ Thu, 13 Apr 2017 13:18:08:  48000000 
INFO  @ Thu, 13 Apr 2017 13:18:09:  49000000 
INFO  @ Thu, 13 Apr 2017 13:18:11:  50000000 
INFO  @ Thu, 13 Apr 2017 13:18:12:  51000000 
INFO  @ Thu, 13 Apr 2017 13:18:13:  52000000 
INFO  @ Thu, 13 Apr 2017 13:18:15:  53000000 
INFO  @ Thu, 13 Apr 2017 13:18:16:  54000000 
INFO  @ Thu, 13 Apr 2017 13:18:17:  55000000 
INFO  @ Thu, 13 Apr 2017 13:18:19:  56000000 
INFO  @ Thu, 13 Apr 2017 13:18:20:  57000000 
INFO  @ Thu, 13 Apr 2017 13:18:22:  58000000 
INFO  @ Thu, 13 Apr 2017 13:18:23:  59000000 
INFO  @ Thu, 13 Apr 2017 13:18:24:  60000000 
INFO  @ Thu, 13 Apr 2017 13:18:26:  61000000 
INFO  @ Thu, 13 Apr 2017 13:18:27:  62000000 
INFO  @ Thu, 13 Apr 2017 13:18:28:  63000000 
INFO  @ Thu, 13 Apr 2017 13:18:30:  64000000 
INFO  @ Thu, 13 Apr 2017 13:18:31:  65000000 
INFO  @ Thu, 13 Apr 2017 13:18:33:  66000000 
INFO  @ Thu, 13 Apr 2017 13:18:34:  67000000 
INFO  @ Thu, 13 Apr 2017 13:18:35:  68000000 
INFO  @ Thu, 13 Apr 2017 13:18:37:  69000000 
INFO  @ Thu, 13 Apr 2017 13:18:38:  70000000 
INFO  @ Thu, 13 Apr 2017 13:18:39:  71000000 
INFO  @ Thu, 13 Apr 2017 13:18:41:  72000000 
INFO  @ Thu, 13 Apr 2017 13:18:42:  73000000 
INFO  @ Thu, 13 Apr 2017 13:18:43:  74000000 
INFO  @ Thu, 13 Apr 2017 13:18:45:  75000000 
INFO  @ Thu, 13 Apr 2017 13:18:46:  76000000 
INFO  @ Thu, 13 Apr 2017 13:18:48:  77000000 
INFO  @ Thu, 13 Apr 2017 13:18:49:  78000000 
INFO  @ Thu, 13 Apr 2017 13:18:50:  79000000 
INFO  @ Thu, 13 Apr 2017 13:18:52:  80000000 
INFO  @ Thu, 13 Apr 2017 13:18:53:  81000000 
INFO  @ Thu, 13 Apr 2017 13:18:54:  82000000 
INFO  @ Thu, 13 Apr 2017 13:18:56:  83000000 
INFO  @ Thu, 13 Apr 2017 13:18:57:  84000000 
INFO  @ Thu, 13 Apr 2017 13:18:59:  85000000 
INFO  @ Thu, 13 Apr 2017 13:19:00:  86000000 
INFO  @ Thu, 13 Apr 2017 13:19:01:  87000000 
INFO  @ Thu, 13 Apr 2017 13:19:03:  88000000 
INFO  @ Thu, 13 Apr 2017 13:19:04:  89000000 
INFO  @ Thu, 13 Apr 2017 13:19:05:  90000000 
INFO  @ Thu, 13 Apr 2017 13:19:07:  91000000 
INFO  @ Thu, 13 Apr 2017 13:19:08:  92000000 
INFO  @ Thu, 13 Apr 2017 13:19:10:  93000000 
INFO  @ Thu, 13 Apr 2017 13:19:11:  94000000 
INFO  @ Thu, 13 Apr 2017 13:19:12:  95000000 
INFO  @ Thu, 13 Apr 2017 13:19:14:  96000000 
INFO  @ Thu, 13 Apr 2017 13:19:15:  97000000 
INFO  @ Thu, 13 Apr 2017 13:19:16:  98000000 
INFO  @ Thu, 13 Apr 2017 13:19:18:  99000000 
INFO  @ Thu, 13 Apr 2017 13:19:19: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:19:19: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:19:19: #1  total tags in treatment: 54211426 
INFO  @ Thu, 13 Apr 2017 13:19:19: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:19:19: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:19:19: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:19:19: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:19:19: #2 Use 213 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:19:19: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:19:19: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:19:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:25:55: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:25:55: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:25:55: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:25:55: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:25:55: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:35:28: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:35:29: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:35:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:35:30: Done!

Num	3
ID	task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12
Name	macs2 n/s ppr2
Thread	thread_Root
PID	46804

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

Start	2017-04-13 13:15:16
End	2017-04-13 13:39:40
Elapsed	00:24:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
12305 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:15:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:15:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:15:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:15:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:15:38:  2000000 
INFO  @ Thu, 13 Apr 2017 13:15:40:  3000000 
INFO  @ Thu, 13 Apr 2017 13:15:42:  4000000 
INFO  @ Thu, 13 Apr 2017 13:15:44:  5000000 
INFO  @ Thu, 13 Apr 2017 13:15:46:  6000000 
INFO  @ Thu, 13 Apr 2017 13:15:49:  7000000 
INFO  @ Thu, 13 Apr 2017 13:15:51:  8000000 
INFO  @ Thu, 13 Apr 2017 13:15:53:  9000000 
INFO  @ Thu, 13 Apr 2017 13:15:55:  10000000 
INFO  @ Thu, 13 Apr 2017 13:15:57:  11000000 
INFO  @ Thu, 13 Apr 2017 13:15:59:  12000000 
INFO  @ Thu, 13 Apr 2017 13:16:01:  13000000 
INFO  @ Thu, 13 Apr 2017 13:16:03:  14000000 
INFO  @ Thu, 13 Apr 2017 13:16:05:  15000000 
INFO  @ Thu, 13 Apr 2017 13:16:07:  16000000 
INFO  @ Thu, 13 Apr 2017 13:16:09:  17000000 
INFO  @ Thu, 13 Apr 2017 13:16:11:  18000000 
INFO  @ Thu, 13 Apr 2017 13:16:13:  19000000 
INFO  @ Thu, 13 Apr 2017 13:16:15:  20000000 
INFO  @ Thu, 13 Apr 2017 13:16:17:  21000000 
INFO  @ Thu, 13 Apr 2017 13:16:19:  22000000 
INFO  @ Thu, 13 Apr 2017 13:16:21:  23000000 
INFO  @ Thu, 13 Apr 2017 13:16:23:  24000000 
INFO  @ Thu, 13 Apr 2017 13:16:25:  25000000 
INFO  @ Thu, 13 Apr 2017 13:16:27:  26000000 
INFO  @ Thu, 13 Apr 2017 13:16:29:  27000000 
INFO  @ Thu, 13 Apr 2017 13:16:31:  28000000 
INFO  @ Thu, 13 Apr 2017 13:16:33:  29000000 
INFO  @ Thu, 13 Apr 2017 13:16:35:  30000000 
INFO  @ Thu, 13 Apr 2017 13:16:37:  31000000 
INFO  @ Thu, 13 Apr 2017 13:16:39:  32000000 
INFO  @ Thu, 13 Apr 2017 13:16:41:  33000000 
INFO  @ Thu, 13 Apr 2017 13:16:43:  34000000 
INFO  @ Thu, 13 Apr 2017 13:16:45:  35000000 
INFO  @ Thu, 13 Apr 2017 13:16:47:  36000000 
INFO  @ Thu, 13 Apr 2017 13:16:49:  37000000 
INFO  @ Thu, 13 Apr 2017 13:16:51:  38000000 
INFO  @ Thu, 13 Apr 2017 13:16:53:  39000000 
INFO  @ Thu, 13 Apr 2017 13:16:55:  40000000 
INFO  @ Thu, 13 Apr 2017 13:16:57:  41000000 
INFO  @ Thu, 13 Apr 2017 13:16:59:  42000000 
INFO  @ Thu, 13 Apr 2017 13:17:01:  43000000 
INFO  @ Thu, 13 Apr 2017 13:17:03:  44000000 
INFO  @ Thu, 13 Apr 2017 13:17:05:  45000000 
INFO  @ Thu, 13 Apr 2017 13:17:06:  46000000 
INFO  @ Thu, 13 Apr 2017 13:17:08:  47000000 
INFO  @ Thu, 13 Apr 2017 13:17:10:  48000000 
INFO  @ Thu, 13 Apr 2017 13:17:12:  49000000 
INFO  @ Thu, 13 Apr 2017 13:17:15:  50000000 
INFO  @ Thu, 13 Apr 2017 13:17:17:  51000000 
INFO  @ Thu, 13 Apr 2017 13:17:19:  52000000 
INFO  @ Thu, 13 Apr 2017 13:17:21:  53000000 
INFO  @ Thu, 13 Apr 2017 13:17:23:  54000000 
INFO  @ Thu, 13 Apr 2017 13:17:28: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:17:30:  1000000 
INFO  @ Thu, 13 Apr 2017 13:17:32:  2000000 
INFO  @ Thu, 13 Apr 2017 13:17:34:  3000000 
INFO  @ Thu, 13 Apr 2017 13:17:36:  4000000 
INFO  @ Thu, 13 Apr 2017 13:17:37:  5000000 
INFO  @ Thu, 13 Apr 2017 13:17:39:  6000000 
INFO  @ Thu, 13 Apr 2017 13:17:41:  7000000 
INFO  @ Thu, 13 Apr 2017 13:17:43:  8000000 
INFO  @ Thu, 13 Apr 2017 13:17:45:  9000000 
INFO  @ Thu, 13 Apr 2017 13:17:47:  10000000 
INFO  @ Thu, 13 Apr 2017 13:17:49:  11000000 
INFO  @ Thu, 13 Apr 2017 13:17:51:  12000000 
INFO  @ Thu, 13 Apr 2017 13:17:53:  13000000 
INFO  @ Thu, 13 Apr 2017 13:17:55:  14000000 
INFO  @ Thu, 13 Apr 2017 13:17:57:  15000000 
INFO  @ Thu, 13 Apr 2017 13:17:59:  16000000 
INFO  @ Thu, 13 Apr 2017 13:18:00:  17000000 
INFO  @ Thu, 13 Apr 2017 13:18:02:  18000000 
INFO  @ Thu, 13 Apr 2017 13:18:04:  19000000 
INFO  @ Thu, 13 Apr 2017 13:18:06:  20000000 
INFO  @ Thu, 13 Apr 2017 13:18:08:  21000000 
INFO  @ Thu, 13 Apr 2017 13:18:10:  22000000 
INFO  @ Thu, 13 Apr 2017 13:18:12:  23000000 
INFO  @ Thu, 13 Apr 2017 13:18:14:  24000000 
INFO  @ Thu, 13 Apr 2017 13:18:16:  25000000 
INFO  @ Thu, 13 Apr 2017 13:18:18:  26000000 
INFO  @ Thu, 13 Apr 2017 13:18:20:  27000000 
INFO  @ Thu, 13 Apr 2017 13:18:22:  28000000 
INFO  @ Thu, 13 Apr 2017 13:18:24:  29000000 
INFO  @ Thu, 13 Apr 2017 13:18:26:  30000000 
INFO  @ Thu, 13 Apr 2017 13:18:27:  31000000 
INFO  @ Thu, 13 Apr 2017 13:18:29:  32000000 
INFO  @ Thu, 13 Apr 2017 13:18:31:  33000000 
INFO  @ Thu, 13 Apr 2017 13:18:33:  34000000 
INFO  @ Thu, 13 Apr 2017 13:18:35:  35000000 
INFO  @ Thu, 13 Apr 2017 13:18:37:  36000000 
INFO  @ Thu, 13 Apr 2017 13:18:39:  37000000 
INFO  @ Thu, 13 Apr 2017 13:18:41:  38000000 
INFO  @ Thu, 13 Apr 2017 13:18:43:  39000000 
INFO  @ Thu, 13 Apr 2017 13:18:45:  40000000 
INFO  @ Thu, 13 Apr 2017 13:18:47:  41000000 
INFO  @ Thu, 13 Apr 2017 13:18:49:  42000000 
INFO  @ Thu, 13 Apr 2017 13:18:50:  43000000 
INFO  @ Thu, 13 Apr 2017 13:18:52:  44000000 
INFO  @ Thu, 13 Apr 2017 13:18:54:  45000000 
INFO  @ Thu, 13 Apr 2017 13:18:56:  46000000 
INFO  @ Thu, 13 Apr 2017 13:18:58:  47000000 
INFO  @ Thu, 13 Apr 2017 13:19:00:  48000000 
INFO  @ Thu, 13 Apr 2017 13:19:02:  49000000 
INFO  @ Thu, 13 Apr 2017 13:19:04:  50000000 
INFO  @ Thu, 13 Apr 2017 13:19:06:  51000000 
INFO  @ Thu, 13 Apr 2017 13:19:08:  52000000 
INFO  @ Thu, 13 Apr 2017 13:19:10:  53000000 
INFO  @ Thu, 13 Apr 2017 13:19:12:  54000000 
INFO  @ Thu, 13 Apr 2017 13:19:14:  55000000 
INFO  @ Thu, 13 Apr 2017 13:19:16:  56000000 
INFO  @ Thu, 13 Apr 2017 13:19:17:  57000000 
INFO  @ Thu, 13 Apr 2017 13:19:19:  58000000 
INFO  @ Thu, 13 Apr 2017 13:19:21:  59000000 
INFO  @ Thu, 13 Apr 2017 13:19:23:  60000000 
INFO  @ Thu, 13 Apr 2017 13:19:25:  61000000 
INFO  @ Thu, 13 Apr 2017 13:19:27:  62000000 
INFO  @ Thu, 13 Apr 2017 13:19:29:  63000000 
INFO  @ Thu, 13 Apr 2017 13:19:31:  64000000 
INFO  @ Thu, 13 Apr 2017 13:19:33:  65000000 
INFO  @ Thu, 13 Apr 2017 13:19:35:  66000000 
INFO  @ Thu, 13 Apr 2017 13:19:37:  67000000 
INFO  @ Thu, 13 Apr 2017 13:19:39:  68000000 
INFO  @ Thu, 13 Apr 2017 13:19:41:  69000000 
INFO  @ Thu, 13 Apr 2017 13:19:43:  70000000 
INFO  @ Thu, 13 Apr 2017 13:19:45:  71000000 
INFO  @ Thu, 13 Apr 2017 13:19:46:  72000000 
INFO  @ Thu, 13 Apr 2017 13:19:48:  73000000 
INFO  @ Thu, 13 Apr 2017 13:19:50:  74000000 
INFO  @ Thu, 13 Apr 2017 13:19:52:  75000000 
INFO  @ Thu, 13 Apr 2017 13:19:54:  76000000 
INFO  @ Thu, 13 Apr 2017 13:19:56:  77000000 
INFO  @ Thu, 13 Apr 2017 13:19:58:  78000000 
INFO  @ Thu, 13 Apr 2017 13:20:00:  79000000 
INFO  @ Thu, 13 Apr 2017 13:20:02:  80000000 
INFO  @ Thu, 13 Apr 2017 13:20:04:  81000000 
INFO  @ Thu, 13 Apr 2017 13:20:06:  82000000 
INFO  @ Thu, 13 Apr 2017 13:20:08:  83000000 
INFO  @ Thu, 13 Apr 2017 13:20:09:  84000000 
INFO  @ Thu, 13 Apr 2017 13:20:11:  85000000 
INFO  @ Thu, 13 Apr 2017 13:20:13:  86000000 
INFO  @ Thu, 13 Apr 2017 13:20:15:  87000000 
INFO  @ Thu, 13 Apr 2017 13:20:17:  88000000 
INFO  @ Thu, 13 Apr 2017 13:20:19:  89000000 
INFO  @ Thu, 13 Apr 2017 13:20:21:  90000000 
INFO  @ Thu, 13 Apr 2017 13:20:23:  91000000 
INFO  @ Thu, 13 Apr 2017 13:20:25:  92000000 
INFO  @ Thu, 13 Apr 2017 13:20:27:  93000000 
INFO  @ Thu, 13 Apr 2017 13:20:28:  94000000 
INFO  @ Thu, 13 Apr 2017 13:20:30:  95000000 
INFO  @ Thu, 13 Apr 2017 13:20:32:  96000000 
INFO  @ Thu, 13 Apr 2017 13:20:34:  97000000 
INFO  @ Thu, 13 Apr 2017 13:20:36:  98000000 
INFO  @ Thu, 13 Apr 2017 13:20:37:  99000000 
INFO  @ Thu, 13 Apr 2017 13:20:39: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:20:39: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:20:39: #1  total tags in treatment: 54211426 
INFO  @ Thu, 13 Apr 2017 13:20:39: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:20:39: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:20:39: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:20:39: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:20:39: #2 Use 213 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:20:39: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:20:39: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:20:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:27:41: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:27:41: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:27:41: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:27:41: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:27:41: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:39:32: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:39:33: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:39:34: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:39:35: Done!

Num	4
ID	task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13
Name	macs2 n/s rep1
Thread	thread_Root
PID	46805

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

Start	2017-04-13 13:15:17
End	2017-04-13 14:52:16
Elapsed	01:36:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1 -o "ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1 -o "ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
46208 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:15:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:15:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:15:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:15:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:15:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:15:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:15:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:15:43:  5000000 
INFO  @ Thu, 13 Apr 2017 13:15:44:  6000000 
INFO  @ Thu, 13 Apr 2017 13:15:46:  7000000 
INFO  @ Thu, 13 Apr 2017 13:15:48:  8000000 
INFO  @ Thu, 13 Apr 2017 13:15:50:  9000000 
INFO  @ Thu, 13 Apr 2017 13:15:51:  10000000 
INFO  @ Thu, 13 Apr 2017 13:15:53:  11000000 
INFO  @ Thu, 13 Apr 2017 13:15:55:  12000000 
INFO  @ Thu, 13 Apr 2017 13:15:58:  13000000 
INFO  @ Thu, 13 Apr 2017 13:15:59:  14000000 
INFO  @ Thu, 13 Apr 2017 13:16:01:  15000000 
INFO  @ Thu, 13 Apr 2017 13:16:03:  16000000 
INFO  @ Thu, 13 Apr 2017 13:16:04:  17000000 
INFO  @ Thu, 13 Apr 2017 13:16:06:  18000000 
INFO  @ Thu, 13 Apr 2017 13:16:08:  19000000 
INFO  @ Thu, 13 Apr 2017 13:16:10:  20000000 
INFO  @ Thu, 13 Apr 2017 13:16:11:  21000000 
INFO  @ Thu, 13 Apr 2017 13:16:13:  22000000 
INFO  @ Thu, 13 Apr 2017 13:16:15:  23000000 
INFO  @ Thu, 13 Apr 2017 13:16:16:  24000000 
INFO  @ Thu, 13 Apr 2017 13:16:18:  25000000 
INFO  @ Thu, 13 Apr 2017 13:16:20:  26000000 
INFO  @ Thu, 13 Apr 2017 13:16:22:  27000000 
INFO  @ Thu, 13 Apr 2017 13:16:23:  28000000 
INFO  @ Thu, 13 Apr 2017 13:16:25:  29000000 
INFO  @ Thu, 13 Apr 2017 13:16:27:  30000000 
INFO  @ Thu, 13 Apr 2017 13:16:29:  31000000 
INFO  @ Thu, 13 Apr 2017 13:16:31:  32000000 
INFO  @ Thu, 13 Apr 2017 13:16:33:  33000000 
INFO  @ Thu, 13 Apr 2017 13:16:35:  34000000 
INFO  @ Thu, 13 Apr 2017 13:16:37:  35000000 
INFO  @ Thu, 13 Apr 2017 13:16:38:  36000000 
INFO  @ Thu, 13 Apr 2017 13:16:40:  37000000 
INFO  @ Thu, 13 Apr 2017 13:16:42:  38000000 
INFO  @ Thu, 13 Apr 2017 13:16:44:  39000000 
INFO  @ Thu, 13 Apr 2017 13:16:45:  40000000 
INFO  @ Thu, 13 Apr 2017 13:16:47:  41000000 
INFO  @ Thu, 13 Apr 2017 13:16:48:  42000000 
INFO  @ Thu, 13 Apr 2017 13:16:50:  43000000 
INFO  @ Thu, 13 Apr 2017 13:16:52:  44000000 
INFO  @ Thu, 13 Apr 2017 13:16:53:  45000000 
INFO  @ Thu, 13 Apr 2017 13:16:55:  46000000 
INFO  @ Thu, 13 Apr 2017 13:16:57:  47000000 
INFO  @ Thu, 13 Apr 2017 13:16:59:  48000000 
INFO  @ Thu, 13 Apr 2017 13:17:01:  49000000 
INFO  @ Thu, 13 Apr 2017 13:17:03:  50000000 
INFO  @ Thu, 13 Apr 2017 13:17:04:  51000000 
INFO  @ Thu, 13 Apr 2017 13:17:06:  52000000 
INFO  @ Thu, 13 Apr 2017 13:17:07:  53000000 
INFO  @ Thu, 13 Apr 2017 13:17:09:  54000000 
INFO  @ Thu, 13 Apr 2017 13:17:13: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:17:15:  1000000 
INFO  @ Thu, 13 Apr 2017 13:17:16:  2000000 
INFO  @ Thu, 13 Apr 2017 13:17:18:  3000000 
INFO  @ Thu, 13 Apr 2017 13:17:19:  4000000 
INFO  @ Thu, 13 Apr 2017 13:17:21:  5000000 
INFO  @ Thu, 13 Apr 2017 13:17:22:  6000000 
INFO  @ Thu, 13 Apr 2017 13:17:24:  7000000 
INFO  @ Thu, 13 Apr 2017 13:17:25:  8000000 
INFO  @ Thu, 13 Apr 2017 13:17:27:  9000000 
INFO  @ Thu, 13 Apr 2017 13:17:28:  10000000 
INFO  @ Thu, 13 Apr 2017 13:17:30:  11000000 
INFO  @ Thu, 13 Apr 2017 13:17:31:  12000000 
INFO  @ Thu, 13 Apr 2017 13:17:33:  13000000 
INFO  @ Thu, 13 Apr 2017 13:17:34:  14000000 
INFO  @ Thu, 13 Apr 2017 13:17:36:  15000000 
INFO  @ Thu, 13 Apr 2017 13:17:37:  16000000 
INFO  @ Thu, 13 Apr 2017 13:17:39:  17000000 
INFO  @ Thu, 13 Apr 2017 13:17:40:  18000000 
INFO  @ Thu, 13 Apr 2017 13:17:41:  19000000 
INFO  @ Thu, 13 Apr 2017 13:17:43:  20000000 
INFO  @ Thu, 13 Apr 2017 13:17:44:  21000000 
INFO  @ Thu, 13 Apr 2017 13:17:46:  22000000 
INFO  @ Thu, 13 Apr 2017 13:17:47:  23000000 
INFO  @ Thu, 13 Apr 2017 13:17:49:  24000000 
INFO  @ Thu, 13 Apr 2017 13:17:50:  25000000 
INFO  @ Thu, 13 Apr 2017 13:17:52:  26000000 
INFO  @ Thu, 13 Apr 2017 13:17:53:  27000000 
INFO  @ Thu, 13 Apr 2017 13:17:55:  28000000 
INFO  @ Thu, 13 Apr 2017 13:17:56:  29000000 
INFO  @ Thu, 13 Apr 2017 13:17:58:  30000000 
INFO  @ Thu, 13 Apr 2017 13:17:59:  31000000 
INFO  @ Thu, 13 Apr 2017 13:18:00:  32000000 
INFO  @ Thu, 13 Apr 2017 13:18:02:  33000000 
INFO  @ Thu, 13 Apr 2017 13:18:03:  34000000 
INFO  @ Thu, 13 Apr 2017 13:18:05:  35000000 
INFO  @ Thu, 13 Apr 2017 13:18:06:  36000000 
INFO  @ Thu, 13 Apr 2017 13:18:08:  37000000 
INFO  @ Thu, 13 Apr 2017 13:18:09:  38000000 
INFO  @ Thu, 13 Apr 2017 13:18:11:  39000000 
INFO  @ Thu, 13 Apr 2017 13:18:12:  40000000 
INFO  @ Thu, 13 Apr 2017 13:18:14:  41000000 
INFO  @ Thu, 13 Apr 2017 13:18:15:  42000000 
INFO  @ Thu, 13 Apr 2017 13:18:17:  43000000 
INFO  @ Thu, 13 Apr 2017 13:18:18:  44000000 
INFO  @ Thu, 13 Apr 2017 13:18:20:  45000000 
INFO  @ Thu, 13 Apr 2017 13:18:21:  46000000 
INFO  @ Thu, 13 Apr 2017 13:18:23:  47000000 
INFO  @ Thu, 13 Apr 2017 13:18:24:  48000000 
INFO  @ Thu, 13 Apr 2017 13:18:26:  49000000 
INFO  @ Thu, 13 Apr 2017 13:18:27:  50000000 
INFO  @ Thu, 13 Apr 2017 13:18:29:  51000000 
INFO  @ Thu, 13 Apr 2017 13:18:30:  52000000 
INFO  @ Thu, 13 Apr 2017 13:18:32:  53000000 
INFO  @ Thu, 13 Apr 2017 13:18:33:  54000000 
INFO  @ Thu, 13 Apr 2017 13:18:35:  55000000 
INFO  @ Thu, 13 Apr 2017 13:18:36:  56000000 
INFO  @ Thu, 13 Apr 2017 13:18:38:  57000000 
INFO  @ Thu, 13 Apr 2017 13:18:39:  58000000 
INFO  @ Thu, 13 Apr 2017 13:18:40:  59000000 
INFO  @ Thu, 13 Apr 2017 13:18:42:  60000000 
INFO  @ Thu, 13 Apr 2017 13:18:44:  61000000 
INFO  @ Thu, 13 Apr 2017 13:18:45:  62000000 
INFO  @ Thu, 13 Apr 2017 13:18:47:  63000000 
INFO  @ Thu, 13 Apr 2017 13:18:49:  64000000 
INFO  @ Thu, 13 Apr 2017 13:18:50:  65000000 
INFO  @ Thu, 13 Apr 2017 13:18:52:  66000000 
INFO  @ Thu, 13 Apr 2017 13:18:53:  67000000 
INFO  @ Thu, 13 Apr 2017 13:18:55:  68000000 
INFO  @ Thu, 13 Apr 2017 13:18:56:  69000000 
INFO  @ Thu, 13 Apr 2017 13:18:58:  70000000 
INFO  @ Thu, 13 Apr 2017 13:18:59:  71000000 
INFO  @ Thu, 13 Apr 2017 13:19:01:  72000000 
INFO  @ Thu, 13 Apr 2017 13:19:02:  73000000 
INFO  @ Thu, 13 Apr 2017 13:19:04:  74000000 
INFO  @ Thu, 13 Apr 2017 13:19:05:  75000000 
INFO  @ Thu, 13 Apr 2017 13:19:07:  76000000 
INFO  @ Thu, 13 Apr 2017 13:19:08:  77000000 
INFO  @ Thu, 13 Apr 2017 13:19:10:  78000000 
INFO  @ Thu, 13 Apr 2017 13:19:11:  79000000 
INFO  @ Thu, 13 Apr 2017 13:19:13:  80000000 
INFO  @ Thu, 13 Apr 2017 13:19:14:  81000000 
INFO  @ Thu, 13 Apr 2017 13:19:16:  82000000 
INFO  @ Thu, 13 Apr 2017 13:19:17:  83000000 
INFO  @ Thu, 13 Apr 2017 13:19:19:  84000000 
INFO  @ Thu, 13 Apr 2017 13:19:20:  85000000 
INFO  @ Thu, 13 Apr 2017 13:19:22:  86000000 
INFO  @ Thu, 13 Apr 2017 13:19:23:  87000000 
INFO  @ Thu, 13 Apr 2017 13:19:25:  88000000 
INFO  @ Thu, 13 Apr 2017 13:19:26:  89000000 
INFO  @ Thu, 13 Apr 2017 13:19:28:  90000000 
INFO  @ Thu, 13 Apr 2017 13:19:29:  91000000 
INFO  @ Thu, 13 Apr 2017 13:19:31:  92000000 
INFO  @ Thu, 13 Apr 2017 13:19:32:  93000000 
INFO  @ Thu, 13 Apr 2017 13:19:33:  94000000 
INFO  @ Thu, 13 Apr 2017 13:19:35:  95000000 
INFO  @ Thu, 13 Apr 2017 13:19:36:  96000000 
INFO  @ Thu, 13 Apr 2017 13:19:38:  97000000 
INFO  @ Thu, 13 Apr 2017 13:19:39:  98000000 
INFO  @ Thu, 13 Apr 2017 13:19:40:  99000000 
INFO  @ Thu, 13 Apr 2017 13:19:42: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:19:42: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:19:42: #1  total tags in treatment: 54689796 
INFO  @ Thu, 13 Apr 2017 13:19:42: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:19:42: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:19:42: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:19:42: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:19:42: #2 Use 215 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:19:42: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:19:42: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:19:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:25:32: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:25:32: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:25:32: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:25:32: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:25:32: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:36:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:36:05: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:36:06: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:36:06: Done! 
INFO  @ Thu, 13 Apr 2017 13:36:09: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:37:56: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:40:37: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 13:41:49: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 13:51:02: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 13:58:15: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:13:18: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:15:15: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:18:25: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:20:21: Values in your input bedGraph files will be multiplied by 54.689796 ... 
INFO  @ Thu, 13 Apr 2017 14:32:17: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 14:34:28: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:39:44: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'!

Num	5
ID	task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14
Name	macs2 n/s rep1-pr1
Thread	thread_Root
PID	46806

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

Start	2017-04-13 13:15:18
End	2017-04-13 13:32:42
Elapsed	00:17:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
46205 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:15:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:15:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:15:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:15:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:15:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:15:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:15:40:  4000000 
INFO  @ Thu, 13 Apr 2017 13:15:42:  5000000 
INFO  @ Thu, 13 Apr 2017 13:15:44:  6000000 
INFO  @ Thu, 13 Apr 2017 13:15:46:  7000000 
INFO  @ Thu, 13 Apr 2017 13:15:48:  8000000 
INFO  @ Thu, 13 Apr 2017 13:15:49:  9000000 
INFO  @ Thu, 13 Apr 2017 13:15:51:  10000000 
INFO  @ Thu, 13 Apr 2017 13:15:53:  11000000 
INFO  @ Thu, 13 Apr 2017 13:15:55:  12000000 
INFO  @ Thu, 13 Apr 2017 13:15:57:  13000000 
INFO  @ Thu, 13 Apr 2017 13:15:59:  14000000 
INFO  @ Thu, 13 Apr 2017 13:16:01:  15000000 
INFO  @ Thu, 13 Apr 2017 13:16:02:  16000000 
INFO  @ Thu, 13 Apr 2017 13:16:04:  17000000 
INFO  @ Thu, 13 Apr 2017 13:16:06:  18000000 
INFO  @ Thu, 13 Apr 2017 13:16:07:  19000000 
INFO  @ Thu, 13 Apr 2017 13:16:09:  20000000 
INFO  @ Thu, 13 Apr 2017 13:16:11:  21000000 
INFO  @ Thu, 13 Apr 2017 13:16:13:  22000000 
INFO  @ Thu, 13 Apr 2017 13:16:14:  23000000 
INFO  @ Thu, 13 Apr 2017 13:16:16:  24000000 
INFO  @ Thu, 13 Apr 2017 13:16:18:  25000000 
INFO  @ Thu, 13 Apr 2017 13:16:19:  26000000 
INFO  @ Thu, 13 Apr 2017 13:16:21:  27000000 
INFO  @ Thu, 13 Apr 2017 13:16:23: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:16:25:  1000000 
INFO  @ Thu, 13 Apr 2017 13:16:27:  2000000 
INFO  @ Thu, 13 Apr 2017 13:16:29:  3000000 
INFO  @ Thu, 13 Apr 2017 13:16:31:  4000000 
INFO  @ Thu, 13 Apr 2017 13:16:33:  5000000 
INFO  @ Thu, 13 Apr 2017 13:16:35:  6000000 
INFO  @ Thu, 13 Apr 2017 13:16:36:  7000000 
INFO  @ Thu, 13 Apr 2017 13:16:37:  8000000 
INFO  @ Thu, 13 Apr 2017 13:16:39:  9000000 
INFO  @ Thu, 13 Apr 2017 13:16:41:  10000000 
INFO  @ Thu, 13 Apr 2017 13:16:42:  11000000 
INFO  @ Thu, 13 Apr 2017 13:16:44:  12000000 
INFO  @ Thu, 13 Apr 2017 13:16:45:  13000000 
INFO  @ Thu, 13 Apr 2017 13:16:47:  14000000 
INFO  @ Thu, 13 Apr 2017 13:16:49:  15000000 
INFO  @ Thu, 13 Apr 2017 13:16:50:  16000000 
INFO  @ Thu, 13 Apr 2017 13:16:52:  17000000 
INFO  @ Thu, 13 Apr 2017 13:16:54:  18000000 
INFO  @ Thu, 13 Apr 2017 13:16:56:  19000000 
INFO  @ Thu, 13 Apr 2017 13:16:57:  20000000 
INFO  @ Thu, 13 Apr 2017 13:16:59:  21000000 
INFO  @ Thu, 13 Apr 2017 13:17:01:  22000000 
INFO  @ Thu, 13 Apr 2017 13:17:02:  23000000 
INFO  @ Thu, 13 Apr 2017 13:17:03:  24000000 
INFO  @ Thu, 13 Apr 2017 13:17:05:  25000000 
INFO  @ Thu, 13 Apr 2017 13:17:06:  26000000 
INFO  @ Thu, 13 Apr 2017 13:17:08:  27000000 
INFO  @ Thu, 13 Apr 2017 13:17:09:  28000000 
INFO  @ Thu, 13 Apr 2017 13:17:11:  29000000 
INFO  @ Thu, 13 Apr 2017 13:17:12:  30000000 
INFO  @ Thu, 13 Apr 2017 13:17:13:  31000000 
INFO  @ Thu, 13 Apr 2017 13:17:15:  32000000 
INFO  @ Thu, 13 Apr 2017 13:17:16:  33000000 
INFO  @ Thu, 13 Apr 2017 13:17:18:  34000000 
INFO  @ Thu, 13 Apr 2017 13:17:19:  35000000 
INFO  @ Thu, 13 Apr 2017 13:17:21:  36000000 
INFO  @ Thu, 13 Apr 2017 13:17:22:  37000000 
INFO  @ Thu, 13 Apr 2017 13:17:24:  38000000 
INFO  @ Thu, 13 Apr 2017 13:17:25:  39000000 
INFO  @ Thu, 13 Apr 2017 13:17:27:  40000000 
INFO  @ Thu, 13 Apr 2017 13:17:28:  41000000 
INFO  @ Thu, 13 Apr 2017 13:17:30:  42000000 
INFO  @ Thu, 13 Apr 2017 13:17:31:  43000000 
INFO  @ Thu, 13 Apr 2017 13:17:33:  44000000 
INFO  @ Thu, 13 Apr 2017 13:17:34:  45000000 
INFO  @ Thu, 13 Apr 2017 13:17:36:  46000000 
INFO  @ Thu, 13 Apr 2017 13:17:37:  47000000 
INFO  @ Thu, 13 Apr 2017 13:17:39:  48000000 
INFO  @ Thu, 13 Apr 2017 13:17:41:  49000000 
INFO  @ Thu, 13 Apr 2017 13:17:42:  50000000 
INFO  @ Thu, 13 Apr 2017 13:17:44:  51000000 
INFO  @ Thu, 13 Apr 2017 13:17:45:  52000000 
INFO  @ Thu, 13 Apr 2017 13:17:47:  53000000 
INFO  @ Thu, 13 Apr 2017 13:17:48:  54000000 
INFO  @ Thu, 13 Apr 2017 13:17:50:  55000000 
INFO  @ Thu, 13 Apr 2017 13:17:51:  56000000 
INFO  @ Thu, 13 Apr 2017 13:17:53:  57000000 
INFO  @ Thu, 13 Apr 2017 13:17:54:  58000000 
INFO  @ Thu, 13 Apr 2017 13:17:56:  59000000 
INFO  @ Thu, 13 Apr 2017 13:17:57:  60000000 
INFO  @ Thu, 13 Apr 2017 13:17:59:  61000000 
INFO  @ Thu, 13 Apr 2017 13:18:00:  62000000 
INFO  @ Thu, 13 Apr 2017 13:18:02:  63000000 
INFO  @ Thu, 13 Apr 2017 13:18:03:  64000000 
INFO  @ Thu, 13 Apr 2017 13:18:05:  65000000 
INFO  @ Thu, 13 Apr 2017 13:18:06:  66000000 
INFO  @ Thu, 13 Apr 2017 13:18:08:  67000000 
INFO  @ Thu, 13 Apr 2017 13:18:10:  68000000 
INFO  @ Thu, 13 Apr 2017 13:18:11:  69000000 
INFO  @ Thu, 13 Apr 2017 13:18:13:  70000000 
INFO  @ Thu, 13 Apr 2017 13:18:14:  71000000 
INFO  @ Thu, 13 Apr 2017 13:18:16:  72000000 
INFO  @ Thu, 13 Apr 2017 13:18:18:  73000000 
INFO  @ Thu, 13 Apr 2017 13:18:19:  74000000 
INFO  @ Thu, 13 Apr 2017 13:18:20:  75000000 
INFO  @ Thu, 13 Apr 2017 13:18:22:  76000000 
INFO  @ Thu, 13 Apr 2017 13:18:23:  77000000 
INFO  @ Thu, 13 Apr 2017 13:18:25:  78000000 
INFO  @ Thu, 13 Apr 2017 13:18:27:  79000000 
INFO  @ Thu, 13 Apr 2017 13:18:28:  80000000 
INFO  @ Thu, 13 Apr 2017 13:18:29:  81000000 
INFO  @ Thu, 13 Apr 2017 13:18:31:  82000000 
INFO  @ Thu, 13 Apr 2017 13:18:32:  83000000 
INFO  @ Thu, 13 Apr 2017 13:18:34:  84000000 
INFO  @ Thu, 13 Apr 2017 13:18:35:  85000000 
INFO  @ Thu, 13 Apr 2017 13:18:37:  86000000 
INFO  @ Thu, 13 Apr 2017 13:18:38:  87000000 
INFO  @ Thu, 13 Apr 2017 13:18:39:  88000000 
INFO  @ Thu, 13 Apr 2017 13:18:41:  89000000 
INFO  @ Thu, 13 Apr 2017 13:18:42:  90000000 
INFO  @ Thu, 13 Apr 2017 13:18:44:  91000000 
INFO  @ Thu, 13 Apr 2017 13:18:45:  92000000 
INFO  @ Thu, 13 Apr 2017 13:18:47:  93000000 
INFO  @ Thu, 13 Apr 2017 13:18:48:  94000000 
INFO  @ Thu, 13 Apr 2017 13:18:50:  95000000 
INFO  @ Thu, 13 Apr 2017 13:18:51:  96000000 
INFO  @ Thu, 13 Apr 2017 13:18:53:  97000000 
INFO  @ Thu, 13 Apr 2017 13:18:55:  98000000 
INFO  @ Thu, 13 Apr 2017 13:18:56:  99000000 
INFO  @ Thu, 13 Apr 2017 13:18:57: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:18:57: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:18:57: #1  total tags in treatment: 27344898 
INFO  @ Thu, 13 Apr 2017 13:18:57: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:18:57: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:18:57: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:18:57: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:18:57: #2 Use 215 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:18:57: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:18:57: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:18:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:24:15: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:24:15: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:24:15: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:24:15: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:24:15: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:32:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:32:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:32:38: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:32:38: Done!

Num	6
ID	task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15
Name	macs2 n/s rep1-pr2
Thread	thread_Root
PID	46834

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

Start	2017-04-13 13:32:45
End	2017-04-13 13:54:21
Elapsed	00:21:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
17748 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:33:03: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:33:03: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:33:03: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:33:06:  1000000 
INFO  @ Thu, 13 Apr 2017 13:33:08:  2000000 
INFO  @ Thu, 13 Apr 2017 13:33:10:  3000000 
INFO  @ Thu, 13 Apr 2017 13:33:12:  4000000 
INFO  @ Thu, 13 Apr 2017 13:33:15:  5000000 
INFO  @ Thu, 13 Apr 2017 13:33:17:  6000000 
INFO  @ Thu, 13 Apr 2017 13:33:19:  7000000 
INFO  @ Thu, 13 Apr 2017 13:33:21:  8000000 
INFO  @ Thu, 13 Apr 2017 13:33:23:  9000000 
INFO  @ Thu, 13 Apr 2017 13:33:25:  10000000 
INFO  @ Thu, 13 Apr 2017 13:33:27:  11000000 
INFO  @ Thu, 13 Apr 2017 13:33:29:  12000000 
INFO  @ Thu, 13 Apr 2017 13:33:31:  13000000 
INFO  @ Thu, 13 Apr 2017 13:33:33:  14000000 
INFO  @ Thu, 13 Apr 2017 13:33:35:  15000000 
INFO  @ Thu, 13 Apr 2017 13:33:37:  16000000 
INFO  @ Thu, 13 Apr 2017 13:33:39:  17000000 
INFO  @ Thu, 13 Apr 2017 13:33:41:  18000000 
INFO  @ Thu, 13 Apr 2017 13:33:43:  19000000 
INFO  @ Thu, 13 Apr 2017 13:33:45:  20000000 
INFO  @ Thu, 13 Apr 2017 13:33:48:  21000000 
INFO  @ Thu, 13 Apr 2017 13:33:50:  22000000 
INFO  @ Thu, 13 Apr 2017 13:33:52:  23000000 
INFO  @ Thu, 13 Apr 2017 13:33:54:  24000000 
INFO  @ Thu, 13 Apr 2017 13:33:56:  25000000 
INFO  @ Thu, 13 Apr 2017 13:33:58:  26000000 
INFO  @ Thu, 13 Apr 2017 13:34:00:  27000000 
INFO  @ Thu, 13 Apr 2017 13:34:03: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:34:05:  1000000 
INFO  @ Thu, 13 Apr 2017 13:34:07:  2000000 
INFO  @ Thu, 13 Apr 2017 13:34:09:  3000000 
INFO  @ Thu, 13 Apr 2017 13:34:10:  4000000 
INFO  @ Thu, 13 Apr 2017 13:34:12:  5000000 
INFO  @ Thu, 13 Apr 2017 13:34:14:  6000000 
INFO  @ Thu, 13 Apr 2017 13:34:16:  7000000 
INFO  @ Thu, 13 Apr 2017 13:34:18:  8000000 
INFO  @ Thu, 13 Apr 2017 13:34:20:  9000000 
INFO  @ Thu, 13 Apr 2017 13:34:22:  10000000 
INFO  @ Thu, 13 Apr 2017 13:34:24:  11000000 
INFO  @ Thu, 13 Apr 2017 13:34:26:  12000000 
INFO  @ Thu, 13 Apr 2017 13:34:28:  13000000 
INFO  @ Thu, 13 Apr 2017 13:34:29:  14000000 
INFO  @ Thu, 13 Apr 2017 13:34:31:  15000000 
INFO  @ Thu, 13 Apr 2017 13:34:33:  16000000 
INFO  @ Thu, 13 Apr 2017 13:34:35:  17000000 
INFO  @ Thu, 13 Apr 2017 13:34:37:  18000000 
INFO  @ Thu, 13 Apr 2017 13:34:39:  19000000 
INFO  @ Thu, 13 Apr 2017 13:34:41:  20000000 
INFO  @ Thu, 13 Apr 2017 13:34:43:  21000000 
INFO  @ Thu, 13 Apr 2017 13:34:45:  22000000 
INFO  @ Thu, 13 Apr 2017 13:34:47:  23000000 
INFO  @ Thu, 13 Apr 2017 13:34:49:  24000000 
INFO  @ Thu, 13 Apr 2017 13:34:50:  25000000 
INFO  @ Thu, 13 Apr 2017 13:34:52:  26000000 
INFO  @ Thu, 13 Apr 2017 13:34:54:  27000000 
INFO  @ Thu, 13 Apr 2017 13:34:56:  28000000 
INFO  @ Thu, 13 Apr 2017 13:34:58:  29000000 
INFO  @ Thu, 13 Apr 2017 13:35:00:  30000000 
INFO  @ Thu, 13 Apr 2017 13:35:02:  31000000 
INFO  @ Thu, 13 Apr 2017 13:35:04:  32000000 
INFO  @ Thu, 13 Apr 2017 13:35:06:  33000000 
INFO  @ Thu, 13 Apr 2017 13:35:08:  34000000 
INFO  @ Thu, 13 Apr 2017 13:35:09:  35000000 
INFO  @ Thu, 13 Apr 2017 13:35:11:  36000000 
INFO  @ Thu, 13 Apr 2017 13:35:13:  37000000 
INFO  @ Thu, 13 Apr 2017 13:35:15:  38000000 
INFO  @ Thu, 13 Apr 2017 13:35:17:  39000000 
INFO  @ Thu, 13 Apr 2017 13:35:19:  40000000 
INFO  @ Thu, 13 Apr 2017 13:35:21:  41000000 
INFO  @ Thu, 13 Apr 2017 13:35:23:  42000000 
INFO  @ Thu, 13 Apr 2017 13:35:24:  43000000 
INFO  @ Thu, 13 Apr 2017 13:35:26:  44000000 
INFO  @ Thu, 13 Apr 2017 13:35:28:  45000000 
INFO  @ Thu, 13 Apr 2017 13:35:30:  46000000 
INFO  @ Thu, 13 Apr 2017 13:35:32:  47000000 
INFO  @ Thu, 13 Apr 2017 13:35:34:  48000000 
INFO  @ Thu, 13 Apr 2017 13:35:36:  49000000 
INFO  @ Thu, 13 Apr 2017 13:35:38:  50000000 
INFO  @ Thu, 13 Apr 2017 13:35:40:  51000000 
INFO  @ Thu, 13 Apr 2017 13:35:41:  52000000 
INFO  @ Thu, 13 Apr 2017 13:35:43:  53000000 
INFO  @ Thu, 13 Apr 2017 13:35:45:  54000000 
INFO  @ Thu, 13 Apr 2017 13:35:47:  55000000 
INFO  @ Thu, 13 Apr 2017 13:35:49:  56000000 
INFO  @ Thu, 13 Apr 2017 13:35:51:  57000000 
INFO  @ Thu, 13 Apr 2017 13:35:53:  58000000 
INFO  @ Thu, 13 Apr 2017 13:35:55:  59000000 
INFO  @ Thu, 13 Apr 2017 13:35:56:  60000000 
INFO  @ Thu, 13 Apr 2017 13:35:58:  61000000 
INFO  @ Thu, 13 Apr 2017 13:36:00:  62000000 
INFO  @ Thu, 13 Apr 2017 13:36:02:  63000000 
INFO  @ Thu, 13 Apr 2017 13:36:04:  64000000 
INFO  @ Thu, 13 Apr 2017 13:36:06:  65000000 
INFO  @ Thu, 13 Apr 2017 13:36:08:  66000000 
INFO  @ Thu, 13 Apr 2017 13:36:10:  67000000 
INFO  @ Thu, 13 Apr 2017 13:36:12:  68000000 
INFO  @ Thu, 13 Apr 2017 13:36:13:  69000000 
INFO  @ Thu, 13 Apr 2017 13:36:15:  70000000 
INFO  @ Thu, 13 Apr 2017 13:36:17:  71000000 
INFO  @ Thu, 13 Apr 2017 13:36:19:  72000000 
INFO  @ Thu, 13 Apr 2017 13:36:21:  73000000 
INFO  @ Thu, 13 Apr 2017 13:36:23:  74000000 
INFO  @ Thu, 13 Apr 2017 13:36:25:  75000000 
INFO  @ Thu, 13 Apr 2017 13:36:27:  76000000 
INFO  @ Thu, 13 Apr 2017 13:36:29:  77000000 
INFO  @ Thu, 13 Apr 2017 13:36:30:  78000000 
INFO  @ Thu, 13 Apr 2017 13:36:32:  79000000 
INFO  @ Thu, 13 Apr 2017 13:36:34:  80000000 
INFO  @ Thu, 13 Apr 2017 13:36:36:  81000000 
INFO  @ Thu, 13 Apr 2017 13:36:38:  82000000 
INFO  @ Thu, 13 Apr 2017 13:36:40:  83000000 
INFO  @ Thu, 13 Apr 2017 13:36:42:  84000000 
INFO  @ Thu, 13 Apr 2017 13:36:44:  85000000 
INFO  @ Thu, 13 Apr 2017 13:36:46:  86000000 
INFO  @ Thu, 13 Apr 2017 13:36:47:  87000000 
INFO  @ Thu, 13 Apr 2017 13:36:49:  88000000 
INFO  @ Thu, 13 Apr 2017 13:36:51:  89000000 
INFO  @ Thu, 13 Apr 2017 13:36:53:  90000000 
INFO  @ Thu, 13 Apr 2017 13:36:55:  91000000 
INFO  @ Thu, 13 Apr 2017 13:36:57:  92000000 
INFO  @ Thu, 13 Apr 2017 13:36:59:  93000000 
INFO  @ Thu, 13 Apr 2017 13:37:01:  94000000 
INFO  @ Thu, 13 Apr 2017 13:37:03:  95000000 
INFO  @ Thu, 13 Apr 2017 13:37:04:  96000000 
INFO  @ Thu, 13 Apr 2017 13:37:06:  97000000 
INFO  @ Thu, 13 Apr 2017 13:37:08:  98000000 
INFO  @ Thu, 13 Apr 2017 13:37:10:  99000000 
INFO  @ Thu, 13 Apr 2017 13:37:12: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:37:12: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:37:12: #1  total tags in treatment: 27344898 
INFO  @ Thu, 13 Apr 2017 13:37:12: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:37:12: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:37:12: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:37:12: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:37:12: #2 Use 215 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:37:12: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:37:12: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:37:12: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:43:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:43:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:43:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:43:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:43:24: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:54:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:54:13: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:54:14: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:54:16: Done!

Num	7
ID	task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16
Name	macs2 n/s rep2
Thread	thread_Root
PID	46844

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

Start	2017-04-13 13:35:36
End	2017-04-13 15:16:16
Elapsed	01:40:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2 -o "ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2 -o "ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
12927 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:36:03: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:36:03: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:36:03: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:36:06:  1000000 
INFO  @ Thu, 13 Apr 2017 13:36:07:  2000000 
INFO  @ Thu, 13 Apr 2017 13:36:09:  3000000 
INFO  @ Thu, 13 Apr 2017 13:36:11:  4000000 
INFO  @ Thu, 13 Apr 2017 13:36:12:  5000000 
INFO  @ Thu, 13 Apr 2017 13:36:14:  6000000 
INFO  @ Thu, 13 Apr 2017 13:36:16:  7000000 
INFO  @ Thu, 13 Apr 2017 13:36:18:  8000000 
INFO  @ Thu, 13 Apr 2017 13:36:19:  9000000 
INFO  @ Thu, 13 Apr 2017 13:36:21:  10000000 
INFO  @ Thu, 13 Apr 2017 13:36:23:  11000000 
INFO  @ Thu, 13 Apr 2017 13:36:25:  12000000 
INFO  @ Thu, 13 Apr 2017 13:36:26:  13000000 
INFO  @ Thu, 13 Apr 2017 13:36:28:  14000000 
INFO  @ Thu, 13 Apr 2017 13:36:29:  15000000 
INFO  @ Thu, 13 Apr 2017 13:36:31:  16000000 
INFO  @ Thu, 13 Apr 2017 13:36:32:  17000000 
INFO  @ Thu, 13 Apr 2017 13:36:34:  18000000 
INFO  @ Thu, 13 Apr 2017 13:36:35:  19000000 
INFO  @ Thu, 13 Apr 2017 13:36:37:  20000000 
INFO  @ Thu, 13 Apr 2017 13:36:38:  21000000 
INFO  @ Thu, 13 Apr 2017 13:36:40:  22000000 
INFO  @ Thu, 13 Apr 2017 13:36:41:  23000000 
INFO  @ Thu, 13 Apr 2017 13:36:43:  24000000 
INFO  @ Thu, 13 Apr 2017 13:36:44:  25000000 
INFO  @ Thu, 13 Apr 2017 13:36:46:  26000000 
INFO  @ Thu, 13 Apr 2017 13:36:47:  27000000 
INFO  @ Thu, 13 Apr 2017 13:36:49:  28000000 
INFO  @ Thu, 13 Apr 2017 13:36:51:  29000000 
INFO  @ Thu, 13 Apr 2017 13:36:52:  30000000 
INFO  @ Thu, 13 Apr 2017 13:36:54:  31000000 
INFO  @ Thu, 13 Apr 2017 13:36:55:  32000000 
INFO  @ Thu, 13 Apr 2017 13:36:57:  33000000 
INFO  @ Thu, 13 Apr 2017 13:36:58:  34000000 
INFO  @ Thu, 13 Apr 2017 13:37:00:  35000000 
INFO  @ Thu, 13 Apr 2017 13:37:02:  36000000 
INFO  @ Thu, 13 Apr 2017 13:37:03:  37000000 
INFO  @ Thu, 13 Apr 2017 13:37:05:  38000000 
INFO  @ Thu, 13 Apr 2017 13:37:06:  39000000 
INFO  @ Thu, 13 Apr 2017 13:37:08:  40000000 
INFO  @ Thu, 13 Apr 2017 13:37:10:  41000000 
INFO  @ Thu, 13 Apr 2017 13:37:11:  42000000 
INFO  @ Thu, 13 Apr 2017 13:37:13:  43000000 
INFO  @ Thu, 13 Apr 2017 13:37:14:  44000000 
INFO  @ Thu, 13 Apr 2017 13:37:16:  45000000 
INFO  @ Thu, 13 Apr 2017 13:37:17:  46000000 
INFO  @ Thu, 13 Apr 2017 13:37:19:  47000000 
INFO  @ Thu, 13 Apr 2017 13:37:20:  48000000 
INFO  @ Thu, 13 Apr 2017 13:37:22:  49000000 
INFO  @ Thu, 13 Apr 2017 13:37:24:  50000000 
INFO  @ Thu, 13 Apr 2017 13:37:25:  51000000 
INFO  @ Thu, 13 Apr 2017 13:37:27:  52000000 
INFO  @ Thu, 13 Apr 2017 13:37:28:  53000000 
INFO  @ Thu, 13 Apr 2017 13:37:33: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:37:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:37:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:37:38:  3000000 
INFO  @ Thu, 13 Apr 2017 13:37:40:  4000000 
INFO  @ Thu, 13 Apr 2017 13:37:41:  5000000 
INFO  @ Thu, 13 Apr 2017 13:37:43:  6000000 
INFO  @ Thu, 13 Apr 2017 13:37:45:  7000000 
INFO  @ Thu, 13 Apr 2017 13:37:46:  8000000 
INFO  @ Thu, 13 Apr 2017 13:37:48:  9000000 
INFO  @ Thu, 13 Apr 2017 13:37:49:  10000000 
INFO  @ Thu, 13 Apr 2017 13:37:51:  11000000 
INFO  @ Thu, 13 Apr 2017 13:37:52:  12000000 
INFO  @ Thu, 13 Apr 2017 13:37:54:  13000000 
INFO  @ Thu, 13 Apr 2017 13:37:55:  14000000 
INFO  @ Thu, 13 Apr 2017 13:37:57:  15000000 
INFO  @ Thu, 13 Apr 2017 13:37:59:  16000000 
INFO  @ Thu, 13 Apr 2017 13:38:00:  17000000 
INFO  @ Thu, 13 Apr 2017 13:38:02:  18000000 
INFO  @ Thu, 13 Apr 2017 13:38:04:  19000000 
INFO  @ Thu, 13 Apr 2017 13:38:05:  20000000 
INFO  @ Thu, 13 Apr 2017 13:38:07:  21000000 
INFO  @ Thu, 13 Apr 2017 13:38:09:  22000000 
INFO  @ Thu, 13 Apr 2017 13:38:11:  23000000 
INFO  @ Thu, 13 Apr 2017 13:38:12:  24000000 
INFO  @ Thu, 13 Apr 2017 13:38:14:  25000000 
INFO  @ Thu, 13 Apr 2017 13:38:16:  26000000 
INFO  @ Thu, 13 Apr 2017 13:38:17:  27000000 
INFO  @ Thu, 13 Apr 2017 13:38:19:  28000000 
INFO  @ Thu, 13 Apr 2017 13:38:20:  29000000 
INFO  @ Thu, 13 Apr 2017 13:38:22:  30000000 
INFO  @ Thu, 13 Apr 2017 13:38:24:  31000000 
INFO  @ Thu, 13 Apr 2017 13:38:25:  32000000 
INFO  @ Thu, 13 Apr 2017 13:38:27:  33000000 
INFO  @ Thu, 13 Apr 2017 13:38:28:  34000000 
INFO  @ Thu, 13 Apr 2017 13:38:30:  35000000 
INFO  @ Thu, 13 Apr 2017 13:38:31:  36000000 
INFO  @ Thu, 13 Apr 2017 13:38:33:  37000000 
INFO  @ Thu, 13 Apr 2017 13:38:35:  38000000 
INFO  @ Thu, 13 Apr 2017 13:38:36:  39000000 
INFO  @ Thu, 13 Apr 2017 13:38:38:  40000000 
INFO  @ Thu, 13 Apr 2017 13:38:39:  41000000 
INFO  @ Thu, 13 Apr 2017 13:38:41:  42000000 
INFO  @ Thu, 13 Apr 2017 13:38:43:  43000000 
INFO  @ Thu, 13 Apr 2017 13:38:44:  44000000 
INFO  @ Thu, 13 Apr 2017 13:38:46:  45000000 
INFO  @ Thu, 13 Apr 2017 13:38:48:  46000000 
INFO  @ Thu, 13 Apr 2017 13:38:49:  47000000 
INFO  @ Thu, 13 Apr 2017 13:38:51:  48000000 
INFO  @ Thu, 13 Apr 2017 13:38:53:  49000000 
INFO  @ Thu, 13 Apr 2017 13:38:54:  50000000 
INFO  @ Thu, 13 Apr 2017 13:38:56:  51000000 
INFO  @ Thu, 13 Apr 2017 13:38:57:  52000000 
INFO  @ Thu, 13 Apr 2017 13:38:59:  53000000 
INFO  @ Thu, 13 Apr 2017 13:39:00:  54000000 
INFO  @ Thu, 13 Apr 2017 13:39:02:  55000000 
INFO  @ Thu, 13 Apr 2017 13:39:03:  56000000 
INFO  @ Thu, 13 Apr 2017 13:39:05:  57000000 
INFO  @ Thu, 13 Apr 2017 13:39:07:  58000000 
INFO  @ Thu, 13 Apr 2017 13:39:08:  59000000 
INFO  @ Thu, 13 Apr 2017 13:39:10:  60000000 
INFO  @ Thu, 13 Apr 2017 13:39:11:  61000000 
INFO  @ Thu, 13 Apr 2017 13:39:13:  62000000 
INFO  @ Thu, 13 Apr 2017 13:39:14:  63000000 
INFO  @ Thu, 13 Apr 2017 13:39:16:  64000000 
INFO  @ Thu, 13 Apr 2017 13:39:17:  65000000 
INFO  @ Thu, 13 Apr 2017 13:39:19:  66000000 
INFO  @ Thu, 13 Apr 2017 13:39:20:  67000000 
INFO  @ Thu, 13 Apr 2017 13:39:22:  68000000 
INFO  @ Thu, 13 Apr 2017 13:39:24:  69000000 
INFO  @ Thu, 13 Apr 2017 13:39:25:  70000000 
INFO  @ Thu, 13 Apr 2017 13:39:27:  71000000 
INFO  @ Thu, 13 Apr 2017 13:39:28:  72000000 
INFO  @ Thu, 13 Apr 2017 13:39:30:  73000000 
INFO  @ Thu, 13 Apr 2017 13:39:31:  74000000 
INFO  @ Thu, 13 Apr 2017 13:39:33:  75000000 
INFO  @ Thu, 13 Apr 2017 13:39:34:  76000000 
INFO  @ Thu, 13 Apr 2017 13:39:35:  77000000 
INFO  @ Thu, 13 Apr 2017 13:39:37:  78000000 
INFO  @ Thu, 13 Apr 2017 13:39:39:  79000000 
INFO  @ Thu, 13 Apr 2017 13:39:40:  80000000 
INFO  @ Thu, 13 Apr 2017 13:39:41:  81000000 
INFO  @ Thu, 13 Apr 2017 13:39:43:  82000000 
INFO  @ Thu, 13 Apr 2017 13:39:44:  83000000 
INFO  @ Thu, 13 Apr 2017 13:39:46:  84000000 
INFO  @ Thu, 13 Apr 2017 13:39:47:  85000000 
INFO  @ Thu, 13 Apr 2017 13:39:49:  86000000 
INFO  @ Thu, 13 Apr 2017 13:39:51:  87000000 
INFO  @ Thu, 13 Apr 2017 13:39:53:  88000000 
INFO  @ Thu, 13 Apr 2017 13:39:54:  89000000 
INFO  @ Thu, 13 Apr 2017 13:39:56:  90000000 
INFO  @ Thu, 13 Apr 2017 13:39:57:  91000000 
INFO  @ Thu, 13 Apr 2017 13:39:59:  92000000 
INFO  @ Thu, 13 Apr 2017 13:40:00:  93000000 
INFO  @ Thu, 13 Apr 2017 13:40:02:  94000000 
INFO  @ Thu, 13 Apr 2017 13:40:03:  95000000 
INFO  @ Thu, 13 Apr 2017 13:40:05:  96000000 
INFO  @ Thu, 13 Apr 2017 13:40:06:  97000000 
INFO  @ Thu, 13 Apr 2017 13:40:08:  98000000 
INFO  @ Thu, 13 Apr 2017 13:40:09:  99000000 
INFO  @ Thu, 13 Apr 2017 13:40:11: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:40:11: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:40:11: #1  total tags in treatment: 53733056 
INFO  @ Thu, 13 Apr 2017 13:40:11: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:40:11: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:40:11: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:40:11: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:40:11: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:40:11: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:40:11: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:40:11: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:00:41: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:00:42: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:00:43: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:00:44: Done! 
INFO  @ Thu, 13 Apr 2017 14:00:47: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:02:24: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:04:57: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:06:20: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:15:34: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:22:18: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:37:43: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:39:14: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:41:42: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:43:18: Values in your input bedGraph files will be multiplied by 53.733056 ... 
INFO  @ Thu, 13 Apr 2017 14:52:25: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 14:54:26: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:59:50: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'!

Num	8
ID	task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17
Name	macs2 n/s rep2-pr1
Thread	thread_Root
PID	46847

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

Start	2017-04-13 13:39:43
End	2017-04-13 13:56:33
Elapsed	00:16:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
16069 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:40:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:40:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:40:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:40:05:  1000000 
INFO  @ Thu, 13 Apr 2017 13:40:07:  2000000 
INFO  @ Thu, 13 Apr 2017 13:40:08:  3000000 
INFO  @ Thu, 13 Apr 2017 13:40:10:  4000000 
INFO  @ Thu, 13 Apr 2017 13:40:12:  5000000 
INFO  @ Thu, 13 Apr 2017 13:40:13:  6000000 
INFO  @ Thu, 13 Apr 2017 13:40:15:  7000000 
INFO  @ Thu, 13 Apr 2017 13:40:17:  8000000 
INFO  @ Thu, 13 Apr 2017 13:40:18:  9000000 
INFO  @ Thu, 13 Apr 2017 13:40:20:  10000000 
INFO  @ Thu, 13 Apr 2017 13:40:21:  11000000 
INFO  @ Thu, 13 Apr 2017 13:40:23:  12000000 
INFO  @ Thu, 13 Apr 2017 13:40:24:  13000000 
INFO  @ Thu, 13 Apr 2017 13:40:26:  14000000 
INFO  @ Thu, 13 Apr 2017 13:40:27:  15000000 
INFO  @ Thu, 13 Apr 2017 13:40:29:  16000000 
INFO  @ Thu, 13 Apr 2017 13:40:30:  17000000 
INFO  @ Thu, 13 Apr 2017 13:40:32:  18000000 
INFO  @ Thu, 13 Apr 2017 13:40:34:  19000000 
INFO  @ Thu, 13 Apr 2017 13:40:35:  20000000 
INFO  @ Thu, 13 Apr 2017 13:40:37:  21000000 
INFO  @ Thu, 13 Apr 2017 13:40:38:  22000000 
INFO  @ Thu, 13 Apr 2017 13:40:40:  23000000 
INFO  @ Thu, 13 Apr 2017 13:40:42:  24000000 
INFO  @ Thu, 13 Apr 2017 13:40:43:  25000000 
INFO  @ Thu, 13 Apr 2017 13:40:45:  26000000 
INFO  @ Thu, 13 Apr 2017 13:40:49: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:40:50:  1000000 
INFO  @ Thu, 13 Apr 2017 13:40:51:  2000000 
INFO  @ Thu, 13 Apr 2017 13:40:53:  3000000 
INFO  @ Thu, 13 Apr 2017 13:40:54:  4000000 
INFO  @ Thu, 13 Apr 2017 13:40:56:  5000000 
INFO  @ Thu, 13 Apr 2017 13:40:57:  6000000 
INFO  @ Thu, 13 Apr 2017 13:40:59:  7000000 
INFO  @ Thu, 13 Apr 2017 13:41:00:  8000000 
INFO  @ Thu, 13 Apr 2017 13:41:01:  9000000 
INFO  @ Thu, 13 Apr 2017 13:41:03:  10000000 
INFO  @ Thu, 13 Apr 2017 13:41:04:  11000000 
INFO  @ Thu, 13 Apr 2017 13:41:06:  12000000 
INFO  @ Thu, 13 Apr 2017 13:41:07:  13000000 
INFO  @ Thu, 13 Apr 2017 13:41:08:  14000000 
INFO  @ Thu, 13 Apr 2017 13:41:10:  15000000 
INFO  @ Thu, 13 Apr 2017 13:41:12:  16000000 
INFO  @ Thu, 13 Apr 2017 13:41:13:  17000000 
INFO  @ Thu, 13 Apr 2017 13:41:14:  18000000 
INFO  @ Thu, 13 Apr 2017 13:41:16:  19000000 
INFO  @ Thu, 13 Apr 2017 13:41:17:  20000000 
INFO  @ Thu, 13 Apr 2017 13:41:19:  21000000 
INFO  @ Thu, 13 Apr 2017 13:41:20:  22000000 
INFO  @ Thu, 13 Apr 2017 13:41:22:  23000000 
INFO  @ Thu, 13 Apr 2017 13:41:23:  24000000 
INFO  @ Thu, 13 Apr 2017 13:41:25:  25000000 
INFO  @ Thu, 13 Apr 2017 13:41:26:  26000000 
INFO  @ Thu, 13 Apr 2017 13:41:27:  27000000 
INFO  @ Thu, 13 Apr 2017 13:41:29:  28000000 
INFO  @ Thu, 13 Apr 2017 13:41:30:  29000000 
INFO  @ Thu, 13 Apr 2017 13:41:32:  30000000 
INFO  @ Thu, 13 Apr 2017 13:41:33:  31000000 
INFO  @ Thu, 13 Apr 2017 13:41:34:  32000000 
INFO  @ Thu, 13 Apr 2017 13:41:36:  33000000 
INFO  @ Thu, 13 Apr 2017 13:41:37:  34000000 
INFO  @ Thu, 13 Apr 2017 13:41:39:  35000000 
INFO  @ Thu, 13 Apr 2017 13:41:40:  36000000 
INFO  @ Thu, 13 Apr 2017 13:41:41:  37000000 
INFO  @ Thu, 13 Apr 2017 13:41:43:  38000000 
INFO  @ Thu, 13 Apr 2017 13:41:44:  39000000 
INFO  @ Thu, 13 Apr 2017 13:41:46:  40000000 
INFO  @ Thu, 13 Apr 2017 13:41:47:  41000000 
INFO  @ Thu, 13 Apr 2017 13:41:49:  42000000 
INFO  @ Thu, 13 Apr 2017 13:41:50:  43000000 
INFO  @ Thu, 13 Apr 2017 13:41:52:  44000000 
INFO  @ Thu, 13 Apr 2017 13:41:53:  45000000 
INFO  @ Thu, 13 Apr 2017 13:41:55:  46000000 
INFO  @ Thu, 13 Apr 2017 13:41:56:  47000000 
INFO  @ Thu, 13 Apr 2017 13:41:57:  48000000 
INFO  @ Thu, 13 Apr 2017 13:41:59:  49000000 
INFO  @ Thu, 13 Apr 2017 13:42:00:  50000000 
INFO  @ Thu, 13 Apr 2017 13:42:02:  51000000 
INFO  @ Thu, 13 Apr 2017 13:42:03:  52000000 
INFO  @ Thu, 13 Apr 2017 13:42:05:  53000000 
INFO  @ Thu, 13 Apr 2017 13:42:06:  54000000 
INFO  @ Thu, 13 Apr 2017 13:42:07:  55000000 
INFO  @ Thu, 13 Apr 2017 13:42:09:  56000000 
INFO  @ Thu, 13 Apr 2017 13:42:10:  57000000 
INFO  @ Thu, 13 Apr 2017 13:42:12:  58000000 
INFO  @ Thu, 13 Apr 2017 13:42:13:  59000000 
INFO  @ Thu, 13 Apr 2017 13:42:14:  60000000 
INFO  @ Thu, 13 Apr 2017 13:42:16:  61000000 
INFO  @ Thu, 13 Apr 2017 13:42:17:  62000000 
INFO  @ Thu, 13 Apr 2017 13:42:19:  63000000 
INFO  @ Thu, 13 Apr 2017 13:42:20:  64000000 
INFO  @ Thu, 13 Apr 2017 13:42:21:  65000000 
INFO  @ Thu, 13 Apr 2017 13:42:23:  66000000 
INFO  @ Thu, 13 Apr 2017 13:42:24:  67000000 
INFO  @ Thu, 13 Apr 2017 13:42:26:  68000000 
INFO  @ Thu, 13 Apr 2017 13:42:27:  69000000 
INFO  @ Thu, 13 Apr 2017 13:42:29:  70000000 
INFO  @ Thu, 13 Apr 2017 13:42:30:  71000000 
INFO  @ Thu, 13 Apr 2017 13:42:31:  72000000 
INFO  @ Thu, 13 Apr 2017 13:42:33:  73000000 
INFO  @ Thu, 13 Apr 2017 13:42:34:  74000000 
INFO  @ Thu, 13 Apr 2017 13:42:36:  75000000 
INFO  @ Thu, 13 Apr 2017 13:42:37:  76000000 
INFO  @ Thu, 13 Apr 2017 13:42:39:  77000000 
INFO  @ Thu, 13 Apr 2017 13:42:40:  78000000 
INFO  @ Thu, 13 Apr 2017 13:42:41:  79000000 
INFO  @ Thu, 13 Apr 2017 13:42:43:  80000000 
INFO  @ Thu, 13 Apr 2017 13:42:44:  81000000 
INFO  @ Thu, 13 Apr 2017 13:42:46:  82000000 
INFO  @ Thu, 13 Apr 2017 13:42:48:  83000000 
INFO  @ Thu, 13 Apr 2017 13:42:49:  84000000 
INFO  @ Thu, 13 Apr 2017 13:42:51:  85000000 
INFO  @ Thu, 13 Apr 2017 13:42:52:  86000000 
INFO  @ Thu, 13 Apr 2017 13:42:54:  87000000 
INFO  @ Thu, 13 Apr 2017 13:42:55:  88000000 
INFO  @ Thu, 13 Apr 2017 13:42:57:  89000000 
INFO  @ Thu, 13 Apr 2017 13:42:58:  90000000 
INFO  @ Thu, 13 Apr 2017 13:43:00:  91000000 
INFO  @ Thu, 13 Apr 2017 13:43:02:  92000000 
INFO  @ Thu, 13 Apr 2017 13:43:03:  93000000 
INFO  @ Thu, 13 Apr 2017 13:43:04:  94000000 
INFO  @ Thu, 13 Apr 2017 13:43:06:  95000000 
INFO  @ Thu, 13 Apr 2017 13:43:07:  96000000 
INFO  @ Thu, 13 Apr 2017 13:43:09:  97000000 
INFO  @ Thu, 13 Apr 2017 13:43:10:  98000000 
INFO  @ Thu, 13 Apr 2017 13:43:11:  99000000 
INFO  @ Thu, 13 Apr 2017 13:43:13: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:43:13: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:43:13: #1  total tags in treatment: 26866528 
INFO  @ Thu, 13 Apr 2017 13:43:13: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:43:13: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:43:13: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:43:13: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:43:13: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:43:13: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:43:13: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:43:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:48:23: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:48:23: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:48:23: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:48:23: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:48:23: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:56:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:56:28: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:56:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:56:29: Done!

Num	9
ID	task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18
Name	macs2 n/s rep2-pr2
Thread	thread_Root
PID	46861

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

Start	2017-04-13 13:54:24
End	2017-04-13 14:11:49
Elapsed	00:17:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

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

   
--------------------Stdout--------------------
34043 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:54:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:54:53: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:54:53: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:54:55:  1000000 
INFO  @ Thu, 13 Apr 2017 13:54:57:  2000000 
INFO  @ Thu, 13 Apr 2017 13:54:59:  3000000 
INFO  @ Thu, 13 Apr 2017 13:55:00:  4000000 
INFO  @ Thu, 13 Apr 2017 13:55:02:  5000000 
INFO  @ Thu, 13 Apr 2017 13:55:03:  6000000 
INFO  @ Thu, 13 Apr 2017 13:55:05:  7000000 
INFO  @ Thu, 13 Apr 2017 13:55:06:  8000000 
INFO  @ Thu, 13 Apr 2017 13:55:08:  9000000 
INFO  @ Thu, 13 Apr 2017 13:55:10:  10000000 
INFO  @ Thu, 13 Apr 2017 13:55:11:  11000000 
INFO  @ Thu, 13 Apr 2017 13:55:13:  12000000 
INFO  @ Thu, 13 Apr 2017 13:55:14:  13000000 
INFO  @ Thu, 13 Apr 2017 13:55:16:  14000000 
INFO  @ Thu, 13 Apr 2017 13:55:18:  15000000 
INFO  @ Thu, 13 Apr 2017 13:55:19:  16000000 
INFO  @ Thu, 13 Apr 2017 13:55:21:  17000000 
INFO  @ Thu, 13 Apr 2017 13:55:22:  18000000 
INFO  @ Thu, 13 Apr 2017 13:55:24:  19000000 
INFO  @ Thu, 13 Apr 2017 13:55:25:  20000000 
INFO  @ Thu, 13 Apr 2017 13:55:27:  21000000 
INFO  @ Thu, 13 Apr 2017 13:55:28:  22000000 
INFO  @ Thu, 13 Apr 2017 13:55:30:  23000000 
INFO  @ Thu, 13 Apr 2017 13:55:31:  24000000 
INFO  @ Thu, 13 Apr 2017 13:55:33:  25000000 
INFO  @ Thu, 13 Apr 2017 13:55:35:  26000000 
INFO  @ Thu, 13 Apr 2017 13:55:38: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:55:40:  1000000 
INFO  @ Thu, 13 Apr 2017 13:55:42:  2000000 
INFO  @ Thu, 13 Apr 2017 13:55:43:  3000000 
INFO  @ Thu, 13 Apr 2017 13:55:44:  4000000 
INFO  @ Thu, 13 Apr 2017 13:55:46:  5000000 
INFO  @ Thu, 13 Apr 2017 13:55:47:  6000000 
INFO  @ Thu, 13 Apr 2017 13:55:49:  7000000 
INFO  @ Thu, 13 Apr 2017 13:55:50:  8000000 
INFO  @ Thu, 13 Apr 2017 13:55:52:  9000000 
INFO  @ Thu, 13 Apr 2017 13:55:53:  10000000 
INFO  @ Thu, 13 Apr 2017 13:55:55:  11000000 
INFO  @ Thu, 13 Apr 2017 13:55:56:  12000000 
INFO  @ Thu, 13 Apr 2017 13:55:57:  13000000 
INFO  @ Thu, 13 Apr 2017 13:55:59:  14000000 
INFO  @ Thu, 13 Apr 2017 13:56:00:  15000000 
INFO  @ Thu, 13 Apr 2017 13:56:02:  16000000 
INFO  @ Thu, 13 Apr 2017 13:56:03:  17000000 
INFO  @ Thu, 13 Apr 2017 13:56:05:  18000000 
INFO  @ Thu, 13 Apr 2017 13:56:06:  19000000 
INFO  @ Thu, 13 Apr 2017 13:56:08:  20000000 
INFO  @ Thu, 13 Apr 2017 13:56:09:  21000000 
INFO  @ Thu, 13 Apr 2017 13:56:10:  22000000 
INFO  @ Thu, 13 Apr 2017 13:56:12:  23000000 
INFO  @ Thu, 13 Apr 2017 13:56:13:  24000000 
INFO  @ Thu, 13 Apr 2017 13:56:15:  25000000 
INFO  @ Thu, 13 Apr 2017 13:56:16:  26000000 
INFO  @ Thu, 13 Apr 2017 13:56:18:  27000000 
INFO  @ Thu, 13 Apr 2017 13:56:19:  28000000 
INFO  @ Thu, 13 Apr 2017 13:56:20:  29000000 
INFO  @ Thu, 13 Apr 2017 13:56:22:  30000000 
INFO  @ Thu, 13 Apr 2017 13:56:23:  31000000 
INFO  @ Thu, 13 Apr 2017 13:56:25:  32000000 
INFO  @ Thu, 13 Apr 2017 13:56:26:  33000000 
INFO  @ Thu, 13 Apr 2017 13:56:28:  34000000 
INFO  @ Thu, 13 Apr 2017 13:56:29:  35000000 
INFO  @ Thu, 13 Apr 2017 13:56:30:  36000000 
INFO  @ Thu, 13 Apr 2017 13:56:32:  37000000 
INFO  @ Thu, 13 Apr 2017 13:56:33:  38000000 
INFO  @ Thu, 13 Apr 2017 13:56:35:  39000000 
INFO  @ Thu, 13 Apr 2017 13:56:36:  40000000 
INFO  @ Thu, 13 Apr 2017 13:56:38:  41000000 
INFO  @ Thu, 13 Apr 2017 13:56:39:  42000000 
INFO  @ Thu, 13 Apr 2017 13:56:40:  43000000 
INFO  @ Thu, 13 Apr 2017 13:56:42:  44000000 
INFO  @ Thu, 13 Apr 2017 13:56:43:  45000000 
INFO  @ Thu, 13 Apr 2017 13:56:44:  46000000 
INFO  @ Thu, 13 Apr 2017 13:56:46:  47000000 
INFO  @ Thu, 13 Apr 2017 13:56:47:  48000000 
INFO  @ Thu, 13 Apr 2017 13:56:49:  49000000 
INFO  @ Thu, 13 Apr 2017 13:56:50:  50000000 
INFO  @ Thu, 13 Apr 2017 13:56:52:  51000000 
INFO  @ Thu, 13 Apr 2017 13:56:53:  52000000 
INFO  @ Thu, 13 Apr 2017 13:56:55:  53000000 
INFO  @ Thu, 13 Apr 2017 13:56:56:  54000000 
INFO  @ Thu, 13 Apr 2017 13:56:58:  55000000 
INFO  @ Thu, 13 Apr 2017 13:56:59:  56000000 
INFO  @ Thu, 13 Apr 2017 13:57:00:  57000000 
INFO  @ Thu, 13 Apr 2017 13:57:02:  58000000 
INFO  @ Thu, 13 Apr 2017 13:57:03:  59000000 
INFO  @ Thu, 13 Apr 2017 13:57:05:  60000000 
INFO  @ Thu, 13 Apr 2017 13:57:06:  61000000 
INFO  @ Thu, 13 Apr 2017 13:57:08:  62000000 
INFO  @ Thu, 13 Apr 2017 13:57:09:  63000000 
INFO  @ Thu, 13 Apr 2017 13:57:10:  64000000 
INFO  @ Thu, 13 Apr 2017 13:57:12:  65000000 
INFO  @ Thu, 13 Apr 2017 13:57:13:  66000000 
INFO  @ Thu, 13 Apr 2017 13:57:15:  67000000 
INFO  @ Thu, 13 Apr 2017 13:57:16:  68000000 
INFO  @ Thu, 13 Apr 2017 13:57:18:  69000000 
INFO  @ Thu, 13 Apr 2017 13:57:19:  70000000 
INFO  @ Thu, 13 Apr 2017 13:57:21:  71000000 
INFO  @ Thu, 13 Apr 2017 13:57:22:  72000000 
INFO  @ Thu, 13 Apr 2017 13:57:24:  73000000 
INFO  @ Thu, 13 Apr 2017 13:57:25:  74000000 
INFO  @ Thu, 13 Apr 2017 13:57:27:  75000000 
INFO  @ Thu, 13 Apr 2017 13:57:28:  76000000 
INFO  @ Thu, 13 Apr 2017 13:57:29:  77000000 
INFO  @ Thu, 13 Apr 2017 13:57:31:  78000000 
INFO  @ Thu, 13 Apr 2017 13:57:33:  79000000 
INFO  @ Thu, 13 Apr 2017 13:57:34:  80000000 
INFO  @ Thu, 13 Apr 2017 13:57:36:  81000000 
INFO  @ Thu, 13 Apr 2017 13:57:37:  82000000 
INFO  @ Thu, 13 Apr 2017 13:57:38:  83000000 
INFO  @ Thu, 13 Apr 2017 13:57:40:  84000000 
INFO  @ Thu, 13 Apr 2017 13:57:41:  85000000 
INFO  @ Thu, 13 Apr 2017 13:57:43:  86000000 
INFO  @ Thu, 13 Apr 2017 13:57:44:  87000000 
INFO  @ Thu, 13 Apr 2017 13:57:45:  88000000 
INFO  @ Thu, 13 Apr 2017 13:57:47:  89000000 
INFO  @ Thu, 13 Apr 2017 13:57:48:  90000000 
INFO  @ Thu, 13 Apr 2017 13:57:50:  91000000 
INFO  @ Thu, 13 Apr 2017 13:57:51:  92000000 
INFO  @ Thu, 13 Apr 2017 13:57:53:  93000000 
INFO  @ Thu, 13 Apr 2017 13:57:54:  94000000 
INFO  @ Thu, 13 Apr 2017 13:57:56:  95000000 
INFO  @ Thu, 13 Apr 2017 13:57:57:  96000000 
INFO  @ Thu, 13 Apr 2017 13:57:58:  97000000 
INFO  @ Thu, 13 Apr 2017 13:58:00:  98000000 
INFO  @ Thu, 13 Apr 2017 13:58:01:  99000000 
INFO  @ Thu, 13 Apr 2017 13:58:03: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:58:03: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:58:03: #1  total tags in treatment: 26866528 
INFO  @ Thu, 13 Apr 2017 13:58:03: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:58:03: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:58:03: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:58:03: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:58:03: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:58:03: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:58:03: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:58:03: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:03:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:03:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:03:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:03:14: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:03:14: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:11:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:11:41: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:11:42: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:11:43: Done!

Num	10
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_19
Name	naive_overlap
Thread	thread_Root
PID	46907

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

Start	2017-04-13 15:54:59
End	2017-04-13 15:56:15
Elapsed	00:01:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 145

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) |    awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 156

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
41260 (process ID) old priority 0, new priority 19
Waiting for 52 seconds.

Num	11
ID	task.callpeak_idr.idr2_rep1_rep2.line_74.id_20
Name	idr2 rep1-rep2
Thread	thread_Root
PID	46908

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

Start	2017-04-13 15:56:17
End	2017-04-13 16:02:36
Elapsed	00:06:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

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

   
--------------------Stdout--------------------
44341 (process ID) old priority 0, new priority 19

Num	12
ID	task.callpeak_idr.idr2_rep1_pr.line_74.id_21
Name	idr2 rep1-pr
Thread	thread_Root
PID	46909

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

Start	2017-04-13 15:56:18
End	2017-04-13 16:00:46
Elapsed	00:04:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

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

   
--------------------Stdout--------------------
44342 (process ID) old priority 0, new priority 19

Num	13
ID	task.callpeak_idr.idr2_rep2_pr.line_74.id_22
Name	idr2 rep2-pr
Thread	thread_Root
PID	46910

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

Start	2017-04-13 15:56:19
End	2017-04-13 16:01:23
Elapsed	00:05:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

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

   
--------------------Stdout--------------------
44344 (process ID) old priority 0, new priority 19

Num	14
ID	task.callpeak_idr.idr2_ppr.line_74.id_23
Name	idr2 ppr
Thread	thread_Root
PID	46911

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

Start	2017-04-13 15:56:20
End	2017-04-13 16:03:09
Elapsed	00:06:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

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

   
--------------------Stdout--------------------
44343 (process ID) old priority 0, new priority 19

Num	15
ID	task.sys.copy_file.line_131.id_32
Name	copy file
Thread	thread_Root
PID	11238

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

Start	2017-04-13 16:03:10
End	2017-04-13 16:03:10
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	16
ID	task.sys.copy_file.line_131.id_33
Name	copy file
Thread	thread_Root
PID	11248

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

Start	2017-04-13 16:03:10
End	2017-04-13 16:03:10
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	17
ID	task.sys.copy_file.line_131.id_34
Name	copy file
Thread	thread_Root
PID	11256

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

Start	2017-04-13 16:03:10
End	2017-04-13 16:03:10
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	18
ID	task.sys.copy_file.line_131.id_35
Name	copy file
Thread	thread_Root
PID	11265

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

Start	2017-04-13 16:03:10
End	2017-04-13 16:03:10
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	19
ID	task.callpeak_idr.idr_final_qc.line_283.id_36
Name	idr final qc
Thread	thread_Root
PID	46912

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

Start	2017-04-13 16:03:12
End	2017-04-13 16:04:30
Elapsed	00:01:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/ZIC2_MACS2_IDR_final.qc
Dependencies

 
# SYS command. line 285

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 287

 echo -e "Nt\tN1	N2	""Np\tN_opt\tN_consv\topt_set\tconsv_set\trescue_ratio\tself_consistency_ratio\treproducibility_test" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/ZIC2_MACS2_IDR_final.qc

# SYS command. line 288

 echo -e "47169\t32735	36145	""47476\t47476\t47169\tpooled_pseudo_rep\trep1-rep2\t1.0065085119464054\t1.1041698487857035\tpass" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/ZIC2_MACS2_IDR_final.qc

# SYS command. line 290

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

   
--------------------Stdout--------------------
11693 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

Num	20
ID	task.callpeak_idr.FRiP_rep1_pr.line_120.id_37
Name	FRiP rep1-pr
Thread	thread_Root
PID	46913

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

Start	2017-04-13 16:03:12
End	2017-04-13 16:06:11
Elapsed	00:02:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -108 -r 108 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

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

   
--------------------Stdout--------------------
19028 (process ID) old priority 0, new priority 19

Num	21
ID	task.callpeak_idr.FRiP_rep2_pr.line_120.id_38
Name	FRiP rep2-pr
Thread	thread_Root
PID	46914

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

Start	2017-04-13 16:03:14
End	2017-04-13 16:05:45
Elapsed	00:02:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -105 -r 105 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

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

   
--------------------Stdout--------------------
11694 (process ID) old priority 0, new priority 19

Num	22
ID	task.callpeak_idr.FRiP_ppr.line_120.id_39
Name	FRiP ppr
Thread	thread_Root
PID	46915

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

Start	2017-04-13 16:03:14
End	2017-04-13 16:08:57
Elapsed	00:05:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -107 -r 107 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZIC2_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

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

   
--------------------Stdout--------------------
19029 (process ID) old priority 0, new priority 19

Num	23
ID	task.callpeak_idr.FRiP_rep1_rep2.line_120.id_40
Name	FRiP rep1-rep2
Thread	thread_Root
PID	46916

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

Start	2017-04-13 16:03:16
End	2017-04-13 16:07:50
Elapsed	00:04:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -107 -r 107 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

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

   
--------------------Stdout--------------------
11695 (process ID) old priority 0, new priority 19

Num	24
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_41
Name	blacklist_filter peak_pooled
Thread	thread_Root
PID	31430

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

Start	2017-04-13 16:08:58
End	2017-04-13 16:10:06
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/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/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
31434 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

Num	25
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_42
Name	blacklist_filter peak 1
Thread	thread_Root
PID	31580

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

Start	2017-04-13 16:09:00
End	2017-04-13 16:10:09
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/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/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
31585 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

Num	26
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_43
Name	blacklist_filter peak 2
Thread	thread_Root
PID	31612

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

Start	2017-04-13 16:09:01
End	2017-04-13 16:10:09
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/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/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
31617 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

Num	27
ID	task.report.peak2hammock.line_361.id_46
Name	peak2hammock
Thread	thread_Root
PID	35837

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

Start	2017-04-13 16:10:10
End	2017-04-13 16:10:20
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/overlap/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
35841 (process ID) old priority 0, new priority 19

Num	28
ID	task.report.peak2hammock.line_361.id_47
Name	peak2hammock
Thread	thread_Root
PID	36416

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

Start	2017-04-13 16:10:21
End	2017-04-13 16:10:30
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/optimal_set/ZIC2_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
36420 (process ID) old priority 0, new priority 19

Num	29
ID	task.report.peak2hammock.line_361.id_48
Name	peak2hammock
Thread	thread_Root
PID	37088

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

Start	2017-04-13 16:10:31
End	2017-04-13 16:10:40
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/conservative_set/ZIC2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
37092 (process ID) old priority 0, new priority 19

Num	30
ID	task.report.peak2hammock.line_361.id_49
Name	peak2hammock
Thread	thread_Root
PID	37744

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

Start	2017-04-13 16:10:41
End	2017-04-13 16:10:52
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZIC2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
37748 (process ID) old priority 0, new priority 19

Num	31
ID	task.report.peak2hammock.line_361.id_50
Name	peak2hammock
Thread	thread_Root
PID	38416

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

Start	2017-04-13 16:10:53
End	2017-04-13 16:11:01
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZIC2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
38420 (process ID) old priority 0, new priority 19

Num	32
ID	task.graphviz.report.line_97.id_51
Name	report
Thread	thread_Root
PID	39004

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

Start	2017-04-13 16:11:02
End	2017-04-13 16:11:16
Elapsed	00:00:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/report/ZIC2_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/report/ZIC2_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/report/ZIC2_MACS2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
39008 (process ID) old priority 0, new priority 19

Num	33
ID	task.report.pdf2png.line_328.id_52
Name	pdf2png
Thread	thread_Root
PID	39068

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

Start	2017-04-13 16:11:03
End	2017-04-13 16:11:16
Elapsed	00:00:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.plot.png
Dependencies

 
# SYS command. line 329

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 330

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.plot.pdf

   
--------------------Stdout--------------------
39074 (process ID) old priority 0, new priority 19

Num	34
ID	task.report.pdf2png.line_328.id_53
Name	pdf2png
Thread	thread_Root
PID	39073

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

Start	2017-04-13 16:11:03
End	2017-04-13 16:11:16
Elapsed	00:00:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.plot.png
Dependencies

 
# SYS command. line 329

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 330

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.plot.pdf

   
--------------------Stdout--------------------
39082 (process ID) old priority 0, new priority 19

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, ZIC2_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZIC2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $]
bool	canFail	false
string	CPATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
string	EVENT_NOEPOLL	1
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_CCx82k
string	LANG	en_US.UTF-8
string	LIBRARY_PATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts//exec:/users/imk1/edirect:/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
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/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
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/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
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	4
string	SSH_CLIENT	171.65.77.8 57066 22
string	SSH_CONNECTION	171.65.77.8 57067 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	45037.ZIC2_MACS2.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	TMUX	/tmp/tmux-1048/default,43619,2
string	TMUX_PANE	%2
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	67062
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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