Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170413_133042_604
Start time	2017-04-13 13:30:42
Run time	00:58:19.393
Tasks executed	18
Tasks failed	0
Tasks failed names
Arguments*	[-title, KLF14_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/KLF14_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -macs2_for_idr, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170413_133042_604/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_10 chipseq.bds.20170413_133042_604/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_11 chipseq.bds.20170413_133042_604/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_12 chipseq.bds.20170413_133042_604/task.callpeak_naive_overlap.naive_overlap.line_59.id_13 chipseq.bds.20170413_133042_604/task.callpeak_idr.idr2_rep1_pr.line_74.id_14 chipseq.bds.20170413_133042_604/task.sys.copy_file.line_131.id_17 chipseq.bds.20170413_133042_604/task.sys.copy_file.line_131.id_18 chipseq.bds.20170413_133042_604/task.sys.copy_file.line_131.id_19 chipseq.bds.20170413_133042_604/task.sys.copy_file.line_131.id_20 chipseq.bds.20170413_133042_604/task.callpeak_idr.idr_final_qc.line_283.id_21 chipseq.bds.20170413_133042_604/task.callpeak_idr.FRiP_rep1_pr.line_120.id_22 chipseq.bds.20170413_133042_604/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_23 chipseq.bds.20170413_133042_604/task.report.peak2hammock.line_361.id_26 chipseq.bds.20170413_133042_604/task.report.peak2hammock.line_361.id_27 chipseq.bds.20170413_133042_604/task.report.peak2hammock.line_361.id_28 chipseq.bds.20170413_133042_604/task.report.peak2hammock.line_361.id_29 chipseq.bds.20170413_133042_604/task.graphviz.report.line_97.id_30 chipseq.bds.20170413_133042_604/task.report.pdf2png.line_328.id_31
thread_41	thread_Root
thread_42	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_n_s_rep1.line_66.id_10
Name	macs2 n/s rep1
Thread	thread_Root
PID	46830

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

Start	2017-04-13 13:30:49
End	2017-04-13 14:20:07
Elapsed	00:49:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/signal/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/signal/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1 -o "SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/signal/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1 -o "SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/signal/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
12573 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:31:05: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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 13:31:05: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:31:05: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:31:07:  1000000 
INFO  @ Thu, 13 Apr 2017 13:31:08:  2000000 
INFO  @ Thu, 13 Apr 2017 13:31:10:  3000000 
INFO  @ Thu, 13 Apr 2017 13:31:11:  4000000 
INFO  @ Thu, 13 Apr 2017 13:31:12:  5000000 
INFO  @ Thu, 13 Apr 2017 13:31:14:  6000000 
INFO  @ Thu, 13 Apr 2017 13:31:15:  7000000 
INFO  @ Thu, 13 Apr 2017 13:31:17:  8000000 
INFO  @ Thu, 13 Apr 2017 13:31:18:  9000000 
INFO  @ Thu, 13 Apr 2017 13:31:19:  10000000 
INFO  @ Thu, 13 Apr 2017 13:31:21:  11000000 
INFO  @ Thu, 13 Apr 2017 13:31:22:  12000000 
INFO  @ Thu, 13 Apr 2017 13:31:23:  13000000 
INFO  @ Thu, 13 Apr 2017 13:31:25:  14000000 
INFO  @ Thu, 13 Apr 2017 13:31:26: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:31:27:  1000000 
INFO  @ Thu, 13 Apr 2017 13:31:29:  2000000 
INFO  @ Thu, 13 Apr 2017 13:31:30:  3000000 
INFO  @ Thu, 13 Apr 2017 13:31:31:  4000000 
INFO  @ Thu, 13 Apr 2017 13:31:33:  5000000 
INFO  @ Thu, 13 Apr 2017 13:31:34:  6000000 
INFO  @ Thu, 13 Apr 2017 13:31:36:  7000000 
INFO  @ Thu, 13 Apr 2017 13:31:37:  8000000 
INFO  @ Thu, 13 Apr 2017 13:31:38:  9000000 
INFO  @ Thu, 13 Apr 2017 13:31:40:  10000000 
INFO  @ Thu, 13 Apr 2017 13:31:41:  11000000 
INFO  @ Thu, 13 Apr 2017 13:31:43:  12000000 
INFO  @ Thu, 13 Apr 2017 13:31:45:  13000000 
INFO  @ Thu, 13 Apr 2017 13:31:46:  14000000 
INFO  @ Thu, 13 Apr 2017 13:31:48:  15000000 
INFO  @ Thu, 13 Apr 2017 13:31:49:  16000000 
INFO  @ Thu, 13 Apr 2017 13:31:51:  17000000 
INFO  @ Thu, 13 Apr 2017 13:31:52:  18000000 
INFO  @ Thu, 13 Apr 2017 13:31:54:  19000000 
INFO  @ Thu, 13 Apr 2017 13:31:55:  20000000 
INFO  @ Thu, 13 Apr 2017 13:31:57:  21000000 
INFO  @ Thu, 13 Apr 2017 13:31:58:  22000000 
INFO  @ Thu, 13 Apr 2017 13:31:59:  23000000 
INFO  @ Thu, 13 Apr 2017 13:32:01:  24000000 
INFO  @ Thu, 13 Apr 2017 13:32:02:  25000000 
INFO  @ Thu, 13 Apr 2017 13:32:04:  26000000 
INFO  @ Thu, 13 Apr 2017 13:32:05:  27000000 
INFO  @ Thu, 13 Apr 2017 13:32:07:  28000000 
INFO  @ Thu, 13 Apr 2017 13:32:08:  29000000 
INFO  @ Thu, 13 Apr 2017 13:32:09:  30000000 
INFO  @ Thu, 13 Apr 2017 13:32:11:  31000000 
INFO  @ Thu, 13 Apr 2017 13:32:12:  32000000 
INFO  @ Thu, 13 Apr 2017 13:32:14:  33000000 
INFO  @ Thu, 13 Apr 2017 13:32:15:  34000000 
INFO  @ Thu, 13 Apr 2017 13:32:16:  35000000 
INFO  @ Thu, 13 Apr 2017 13:32:18:  36000000 
INFO  @ Thu, 13 Apr 2017 13:32:19:  37000000 
INFO  @ Thu, 13 Apr 2017 13:32:21:  38000000 
INFO  @ Thu, 13 Apr 2017 13:32:22:  39000000 
INFO  @ Thu, 13 Apr 2017 13:32:24:  40000000 
INFO  @ Thu, 13 Apr 2017 13:32:25:  41000000 
INFO  @ Thu, 13 Apr 2017 13:32:26:  42000000 
INFO  @ Thu, 13 Apr 2017 13:32:28:  43000000 
INFO  @ Thu, 13 Apr 2017 13:32:29:  44000000 
INFO  @ Thu, 13 Apr 2017 13:32:31:  45000000 
INFO  @ Thu, 13 Apr 2017 13:32:32:  46000000 
INFO  @ Thu, 13 Apr 2017 13:32:33:  47000000 
INFO  @ Thu, 13 Apr 2017 13:32:35:  48000000 
INFO  @ Thu, 13 Apr 2017 13:32:36:  49000000 
INFO  @ Thu, 13 Apr 2017 13:32:38:  50000000 
INFO  @ Thu, 13 Apr 2017 13:32:39: #1 tag size is determined as 68 bps 
INFO  @ Thu, 13 Apr 2017 13:32:39: #1 tag size = 68 
INFO  @ Thu, 13 Apr 2017 13:32:39: #1  total tags in treatment: 14380722 
INFO  @ Thu, 13 Apr 2017 13:32:39: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 13:32:39: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:32:39: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:32:39: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:32:39: #2 Use 150 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:32:39: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:32:39: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:32:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:36:03: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:36:03: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:03: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:03: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:36:03: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:41:04: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:41:06: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:41:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:41:10: Done! 
INFO  @ Thu, 13 Apr 2017 13:41:14: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:41:49: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:43:49: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 13:44:43: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 13:49:49: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 13:52:10: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 13:58:56: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:59:30: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:01:32: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:02:25: Values in your input bedGraph files will be multiplied by 14.380722 ... 
INFO  @ Thu, 13 Apr 2017 14:07:21: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 14:07:58: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:10:55: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'!

Num	2
ID	task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_11
Name	macs2 n/s rep1-pr1
Thread	thread_Root
PID	46831

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

Start	2017-04-13 13:30:50
End	2017-04-13 13:40:10
Elapsed	00:09:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
20897 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:31:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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 13:31:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:31:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:31:04:  1000000 
INFO  @ Thu, 13 Apr 2017 13:31:06:  2000000 
INFO  @ Thu, 13 Apr 2017 13:31:07:  3000000 
INFO  @ Thu, 13 Apr 2017 13:31:09:  4000000 
INFO  @ Thu, 13 Apr 2017 13:31:11:  5000000 
INFO  @ Thu, 13 Apr 2017 13:31:13:  6000000 
INFO  @ Thu, 13 Apr 2017 13:31:14:  7000000 
INFO  @ Thu, 13 Apr 2017 13:31:15: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:31:17:  1000000 
INFO  @ Thu, 13 Apr 2017 13:31:18:  2000000 
INFO  @ Thu, 13 Apr 2017 13:31:20:  3000000 
INFO  @ Thu, 13 Apr 2017 13:31:22:  4000000 
INFO  @ Thu, 13 Apr 2017 13:31:24:  5000000 
INFO  @ Thu, 13 Apr 2017 13:31:25:  6000000 
INFO  @ Thu, 13 Apr 2017 13:31:27:  7000000 
INFO  @ Thu, 13 Apr 2017 13:31:28:  8000000 
INFO  @ Thu, 13 Apr 2017 13:31:30:  9000000 
INFO  @ Thu, 13 Apr 2017 13:31:31:  10000000 
INFO  @ Thu, 13 Apr 2017 13:31:33:  11000000 
INFO  @ Thu, 13 Apr 2017 13:31:35:  12000000 
INFO  @ Thu, 13 Apr 2017 13:31:36:  13000000 
INFO  @ Thu, 13 Apr 2017 13:31:37:  14000000 
INFO  @ Thu, 13 Apr 2017 13:31:39:  15000000 
INFO  @ Thu, 13 Apr 2017 13:31:41:  16000000 
INFO  @ Thu, 13 Apr 2017 13:31:42:  17000000 
INFO  @ Thu, 13 Apr 2017 13:31:44:  18000000 
INFO  @ Thu, 13 Apr 2017 13:31:45:  19000000 
INFO  @ Thu, 13 Apr 2017 13:31:47:  20000000 
INFO  @ Thu, 13 Apr 2017 13:31:48:  21000000 
INFO  @ Thu, 13 Apr 2017 13:31:50:  22000000 
INFO  @ Thu, 13 Apr 2017 13:31:51:  23000000 
INFO  @ Thu, 13 Apr 2017 13:31:52:  24000000 
INFO  @ Thu, 13 Apr 2017 13:31:54:  25000000 
INFO  @ Thu, 13 Apr 2017 13:31:55:  26000000 
INFO  @ Thu, 13 Apr 2017 13:31:57:  27000000 
INFO  @ Thu, 13 Apr 2017 13:31:58:  28000000 
INFO  @ Thu, 13 Apr 2017 13:32:00:  29000000 
INFO  @ Thu, 13 Apr 2017 13:32:02:  30000000 
INFO  @ Thu, 13 Apr 2017 13:32:03:  31000000 
INFO  @ Thu, 13 Apr 2017 13:32:05:  32000000 
INFO  @ Thu, 13 Apr 2017 13:32:06:  33000000 
INFO  @ Thu, 13 Apr 2017 13:32:08:  34000000 
INFO  @ Thu, 13 Apr 2017 13:32:09:  35000000 
INFO  @ Thu, 13 Apr 2017 13:32:11:  36000000 
INFO  @ Thu, 13 Apr 2017 13:32:12:  37000000 
INFO  @ Thu, 13 Apr 2017 13:32:14:  38000000 
INFO  @ Thu, 13 Apr 2017 13:32:15:  39000000 
INFO  @ Thu, 13 Apr 2017 13:32:17:  40000000 
INFO  @ Thu, 13 Apr 2017 13:32:18:  41000000 
INFO  @ Thu, 13 Apr 2017 13:32:20:  42000000 
INFO  @ Thu, 13 Apr 2017 13:32:21:  43000000 
INFO  @ Thu, 13 Apr 2017 13:32:23:  44000000 
INFO  @ Thu, 13 Apr 2017 13:32:25:  45000000 
INFO  @ Thu, 13 Apr 2017 13:32:26:  46000000 
INFO  @ Thu, 13 Apr 2017 13:32:28:  47000000 
INFO  @ Thu, 13 Apr 2017 13:32:29:  48000000 
INFO  @ Thu, 13 Apr 2017 13:32:31:  49000000 
INFO  @ Thu, 13 Apr 2017 13:32:32:  50000000 
INFO  @ Thu, 13 Apr 2017 13:32:34: #1 tag size is determined as 67 bps 
INFO  @ Thu, 13 Apr 2017 13:32:34: #1 tag size = 67 
INFO  @ Thu, 13 Apr 2017 13:32:34: #1  total tags in treatment: 7190361 
INFO  @ Thu, 13 Apr 2017 13:32:34: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 13:32:34: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:32:34: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:32:34: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:32:34: #2 Use 150 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:32:34: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:32:34: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:32:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:35:20: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:35:20: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:35:20: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:35:20: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:35:20: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:39:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:39:56: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:39:58: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:40:03: Done!

Num	3
ID	task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_12
Name	macs2 n/s rep1-pr2
Thread	thread_Root
PID	46832

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

Start	2017-04-13 13:30:51
End	2017-04-13 13:41:45
Elapsed	00:10:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
17169 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:31:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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 13:31:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:31:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:31:19:  1000000 
INFO  @ Thu, 13 Apr 2017 13:31:21:  2000000 
INFO  @ Thu, 13 Apr 2017 13:31:23:  3000000 
INFO  @ Thu, 13 Apr 2017 13:31:25:  4000000 
INFO  @ Thu, 13 Apr 2017 13:31:28:  5000000 
INFO  @ Thu, 13 Apr 2017 13:31:30:  6000000 
INFO  @ Thu, 13 Apr 2017 13:31:32:  7000000 
INFO  @ Thu, 13 Apr 2017 13:31:33: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:31:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:31:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:31:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:31:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:31:43:  5000000 
INFO  @ Thu, 13 Apr 2017 13:31:47:  6000000 
INFO  @ Thu, 13 Apr 2017 13:31:49:  7000000 
INFO  @ Thu, 13 Apr 2017 13:31:51:  8000000 
INFO  @ Thu, 13 Apr 2017 13:31:53:  9000000 
INFO  @ Thu, 13 Apr 2017 13:31:55:  10000000 
INFO  @ Thu, 13 Apr 2017 13:31:57:  11000000 
INFO  @ Thu, 13 Apr 2017 13:31:59:  12000000 
INFO  @ Thu, 13 Apr 2017 13:32:01:  13000000 
INFO  @ Thu, 13 Apr 2017 13:32:03:  14000000 
INFO  @ Thu, 13 Apr 2017 13:32:05:  15000000 
INFO  @ Thu, 13 Apr 2017 13:32:07:  16000000 
INFO  @ Thu, 13 Apr 2017 13:32:09:  17000000 
INFO  @ Thu, 13 Apr 2017 13:32:11:  18000000 
INFO  @ Thu, 13 Apr 2017 13:32:13:  19000000 
INFO  @ Thu, 13 Apr 2017 13:32:15:  20000000 
INFO  @ Thu, 13 Apr 2017 13:32:17:  21000000 
INFO  @ Thu, 13 Apr 2017 13:32:19:  22000000 
INFO  @ Thu, 13 Apr 2017 13:32:21:  23000000 
INFO  @ Thu, 13 Apr 2017 13:32:23:  24000000 
INFO  @ Thu, 13 Apr 2017 13:32:25:  25000000 
INFO  @ Thu, 13 Apr 2017 13:32:27:  26000000 
INFO  @ Thu, 13 Apr 2017 13:32:29:  27000000 
INFO  @ Thu, 13 Apr 2017 13:32:31:  28000000 
INFO  @ Thu, 13 Apr 2017 13:32:33:  29000000 
INFO  @ Thu, 13 Apr 2017 13:32:35:  30000000 
INFO  @ Thu, 13 Apr 2017 13:32:37:  31000000 
INFO  @ Thu, 13 Apr 2017 13:32:39:  32000000 
INFO  @ Thu, 13 Apr 2017 13:32:41:  33000000 
INFO  @ Thu, 13 Apr 2017 13:32:42:  34000000 
INFO  @ Thu, 13 Apr 2017 13:32:44:  35000000 
INFO  @ Thu, 13 Apr 2017 13:32:46:  36000000 
INFO  @ Thu, 13 Apr 2017 13:32:48:  37000000 
INFO  @ Thu, 13 Apr 2017 13:32:50:  38000000 
INFO  @ Thu, 13 Apr 2017 13:32:52:  39000000 
INFO  @ Thu, 13 Apr 2017 13:32:54:  40000000 
INFO  @ Thu, 13 Apr 2017 13:32:56:  41000000 
INFO  @ Thu, 13 Apr 2017 13:32:58:  42000000 
INFO  @ Thu, 13 Apr 2017 13:33:00:  43000000 
INFO  @ Thu, 13 Apr 2017 13:33:02:  44000000 
INFO  @ Thu, 13 Apr 2017 13:33:04:  45000000 
INFO  @ Thu, 13 Apr 2017 13:33:06:  46000000 
INFO  @ Thu, 13 Apr 2017 13:33:08:  47000000 
INFO  @ Thu, 13 Apr 2017 13:33:10:  48000000 
INFO  @ Thu, 13 Apr 2017 13:33:12:  49000000 
INFO  @ Thu, 13 Apr 2017 13:33:14:  50000000 
INFO  @ Thu, 13 Apr 2017 13:33:16: #1 tag size is determined as 68 bps 
INFO  @ Thu, 13 Apr 2017 13:33:16: #1 tag size = 68 
INFO  @ Thu, 13 Apr 2017 13:33:16: #1  total tags in treatment: 7190361 
INFO  @ Thu, 13 Apr 2017 13:33:16: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 13:33:16: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:33:16: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:33:16: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:33:16: #2 Use 150 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:33:16: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:33:16: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:33:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:36:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:36:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:14: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:36:14: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:41:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:41:39: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:41:40: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:41:41: Done!

Num	4
ID	task.callpeak_naive_overlap.naive_overlap.line_59.id_13
Name	naive_overlap
Thread	thread_Root
PID	46875

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

Start	2017-04-13 14:20:08
End	2017-04-13 14:21:30
Elapsed	00:01:22
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 61

 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 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 72

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.narrowPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 76

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

   
--------------------Stdout--------------------
52679 (process ID) old priority 0, new priority 19
Waiting for 56 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	172955	173349	Peak_1089	292	.	15.36934	29.26207	24.73599	156

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	172955	173349	Peak_1089	292	.	15.36934	29.26207	24.73599	156

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270733.1	168733	169118	Peak_1655	255	.	9.47463	25.51725	21.20995	137

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270733.1	168733	169118	Peak_1655	255	.	9.47463	25.51725	21.20995	137

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000009.2	124712	124997	Peak_16339	139	.	8.33829	13.90367	10.81646	138

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000009.2	124712	124997	Peak_16339	139	.	8.33829	13.90367	10.81646	138

Num	5
ID	task.callpeak_idr.idr2_rep1_pr.line_74.id_14
Name	idr2 rep1-pr
Thread	thread_Root
PID	46876

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

Start	2017-04-13 14:21:32
End	2017-04-13 14:25:41
Elapsed	00:04:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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--------------------
55601 (process ID) old priority 0, new priority 19

Num	6
ID	task.sys.copy_file.line_131.id_17
Name	copy file
Thread	thread_Root
PID	8579

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

Start	2017-04-13 14:25:42
End	2017-04-13 14:25:42
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	7
ID	task.sys.copy_file.line_131.id_18
Name	copy file
Thread	thread_Root
PID	8581

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

Start	2017-04-13 14:25:42
End	2017-04-13 14:25:42
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	8
ID	task.sys.copy_file.line_131.id_19
Name	copy file
Thread	thread_Root
PID	8598

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

Start	2017-04-13 14:25:42
End	2017-04-13 14:25:42
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	9
ID	task.sys.copy_file.line_131.id_20
Name	copy file
Thread	thread_Root
PID	8612

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

Start	2017-04-13 14:25:42
End	2017-04-13 14:25:42
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	10
ID	task.callpeak_idr.idr_final_qc.line_283.id_21
Name	idr final qc
Thread	thread_Root
PID	46883

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

Start	2017-04-13 14:25:44
End	2017-04-13 14:27:00
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/qc/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/qc/KLF14_MACS2_IDR_final.qc

# SYS command. line 288

 echo -e "0\t25364	0	""0\t25364\t25364\tself_pseudo_rep_rep1\tself_pseudo_rep_rep1\t0.0\t1.0\tpass" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/qc/KLF14_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--------------------
50565 (process ID) old priority 0, new priority 19
Waiting for 58 seconds.

Num	11
ID	task.callpeak_idr.FRiP_rep1_pr.line_120.id_22
Name	FRiP rep1-pr
Thread	thread_Root
PID	46884

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

Start	2017-04-13 14:25:45
End	2017-04-13 14:27:01
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -s -l -75 -r 75 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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--------------------
50566 (process ID) old priority 0, new priority 19
Waiting for 17 seconds.

 
--------------------Stderr--------------------
***** WARNING: File stdin has inconsistent naming convention for record:
GL000008.2	96	165	N	1000	+

***** WARNING: File stdin has inconsistent naming convention for record:
GL000008.2	96	165	N	1000	+

Num	12
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_23
Name	blacklist_filter peak 1
Thread	thread_Root
PID	11666

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

Start	2017-04-13 14:27:02
End	2017-04-13 14:28:10
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
11670 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270733.1	172954	173349	Peak_1233	491	.	20.93574	49.17350	44.76045	145

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270733.1	172954	173349	Peak_1233	491	.	20.93574	49.17350	44.76045	145

Num	13
ID	task.report.peak2hammock.line_361.id_26
Name	peak2hammock
Thread	thread_Root
PID	14538

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

Start	2017-04-13 14:28:11
End	2017-04-13 14:28:20
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
14542 (process ID) old priority 0, new priority 19

Num	14
ID	task.report.peak2hammock.line_361.id_27
Name	peak2hammock
Thread	thread_Root
PID	15020

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

Start	2017-04-13 14:28:21
End	2017-04-13 14:28:31
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/optimal_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
15024 (process ID) old priority 0, new priority 19

Num	15
ID	task.report.peak2hammock.line_361.id_28
Name	peak2hammock
Thread	thread_Root
PID	15647

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

Start	2017-04-13 14:28:32
End	2017-04-13 14:28:40
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/conservative_set/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
15651 (process ID) old priority 0, new priority 19

Num	16
ID	task.report.peak2hammock.line_361.id_29
Name	peak2hammock
Thread	thread_Root
PID	16058

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

Start	2017-04-13 14:28:41
End	2017-04-13 14:28:52
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/KLF14_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
16062 (process ID) old priority 0, new priority 19

Num	17
ID	task.graphviz.report.line_97.id_30
Name	report
Thread	thread_Root
PID	16550

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

Start	2017-04-13 14:28:53
End	2017-04-13 14:29:00
Elapsed	00:00:07
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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/report/KLF14_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/report/KLF14_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/report/KLF14_MACS2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
16554 (process ID) old priority 0, new priority 19

Num	18
ID	task.report.pdf2png.line_328.id_31
Name	pdf2png
Thread	thread_Root
PID	16568

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

Start	2017-04-13 14:28:53
End	2017-04-13 14:29:01
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/qc/rep1/SRR1370885_1.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/qc/rep1/SRR1370885_1.nodup.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/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/qc/rep1/SRR1370885_1.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/qc/rep1/SRR1370885_1.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
16572 (process ID) old priority 0, new priority 19

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, KLF14_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/KLF14_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -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/Najafabadi2015Data/hg38Mapping/KLF14_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/Najafabadi2015Data/hg38Mapping/KLF14_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	51289.KLF14_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

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope