Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170413_133523_572
Start time	2017-04-13 13:35:23
Run time	01:02:13.110
Tasks executed	18
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF467_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF467_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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_133523_572/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_10 chipseq.bds.20170413_133523_572/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_11 chipseq.bds.20170413_133523_572/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_12 chipseq.bds.20170413_133523_572/task.callpeak_naive_overlap.naive_overlap.line_59.id_13 chipseq.bds.20170413_133523_572/task.callpeak_idr.idr2_rep1_pr.line_74.id_14 chipseq.bds.20170413_133523_572/task.sys.copy_file.line_131.id_17 chipseq.bds.20170413_133523_572/task.sys.copy_file.line_131.id_18 chipseq.bds.20170413_133523_572/task.sys.copy_file.line_131.id_19 chipseq.bds.20170413_133523_572/task.sys.copy_file.line_131.id_20 chipseq.bds.20170413_133523_572/task.callpeak_idr.idr_final_qc.line_283.id_21 chipseq.bds.20170413_133523_572/task.callpeak_idr.FRiP_rep1_pr.line_120.id_22 chipseq.bds.20170413_133523_572/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_23 chipseq.bds.20170413_133523_572/task.report.peak2hammock.line_361.id_26 chipseq.bds.20170413_133523_572/task.report.peak2hammock.line_361.id_27 chipseq.bds.20170413_133523_572/task.report.peak2hammock.line_361.id_28 chipseq.bds.20170413_133523_572/task.report.peak2hammock.line_361.id_29 chipseq.bds.20170413_133523_572/task.graphviz.report.line_97.id_30 chipseq.bds.20170413_133523_572/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	46841

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

Start	2017-04-13 13:35:30
End	2017-04-13 14:26:33
Elapsed	00:51:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/signal/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/signal/macs2/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1 -o "SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/signal/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1 -o "SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/signal/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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--------------------
12832 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:35:48: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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 13:35:48: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:35:48: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:35:50:  1000000 
INFO  @ Thu, 13 Apr 2017 13:35:52:  2000000 
INFO  @ Thu, 13 Apr 2017 13:35:53:  3000000 
INFO  @ Thu, 13 Apr 2017 13:35:54:  4000000 
INFO  @ Thu, 13 Apr 2017 13:35:56:  5000000 
INFO  @ Thu, 13 Apr 2017 13:35:58:  6000000 
INFO  @ Thu, 13 Apr 2017 13:35:59:  7000000 
INFO  @ Thu, 13 Apr 2017 13:36:00:  8000000 
INFO  @ Thu, 13 Apr 2017 13:36:02:  9000000 
INFO  @ Thu, 13 Apr 2017 13:36:03:  10000000 
INFO  @ Thu, 13 Apr 2017 13:36:05:  11000000 
INFO  @ Thu, 13 Apr 2017 13:36:06:  12000000 
INFO  @ Thu, 13 Apr 2017 13:36:08:  13000000 
INFO  @ Thu, 13 Apr 2017 13:36:09:  14000000 
INFO  @ Thu, 13 Apr 2017 13:36:11:  15000000 
INFO  @ Thu, 13 Apr 2017 13:36:12:  16000000 
INFO  @ Thu, 13 Apr 2017 13:36:13:  17000000 
INFO  @ Thu, 13 Apr 2017 13:36:15:  18000000 
INFO  @ Thu, 13 Apr 2017 13:36:15: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:36:17:  1000000 
INFO  @ Thu, 13 Apr 2017 13:36:19:  2000000 
INFO  @ Thu, 13 Apr 2017 13:36:20:  3000000 
INFO  @ Thu, 13 Apr 2017 13:36:21:  4000000 
INFO  @ Thu, 13 Apr 2017 13:36:23:  5000000 
INFO  @ Thu, 13 Apr 2017 13:36:24:  6000000 
INFO  @ Thu, 13 Apr 2017 13:36:26:  7000000 
INFO  @ Thu, 13 Apr 2017 13:36:27:  8000000 
INFO  @ Thu, 13 Apr 2017 13:36:29:  9000000 
INFO  @ Thu, 13 Apr 2017 13:36:31:  10000000 
INFO  @ Thu, 13 Apr 2017 13:36:32:  11000000 
INFO  @ Thu, 13 Apr 2017 13:36:34:  12000000 
INFO  @ Thu, 13 Apr 2017 13:36:35:  13000000 
INFO  @ Thu, 13 Apr 2017 13:36:37:  14000000 
INFO  @ Thu, 13 Apr 2017 13:36:38:  15000000 
INFO  @ Thu, 13 Apr 2017 13:36:39:  16000000 
INFO  @ Thu, 13 Apr 2017 13:36:41:  17000000 
INFO  @ Thu, 13 Apr 2017 13:36:42:  18000000 
INFO  @ Thu, 13 Apr 2017 13:36:44:  19000000 
INFO  @ Thu, 13 Apr 2017 13:36:45:  20000000 
INFO  @ Thu, 13 Apr 2017 13:36:47:  21000000 
INFO  @ Thu, 13 Apr 2017 13:36:48:  22000000 
INFO  @ Thu, 13 Apr 2017 13:36:49:  23000000 
INFO  @ Thu, 13 Apr 2017 13:36:51:  24000000 
INFO  @ Thu, 13 Apr 2017 13:36:52:  25000000 
INFO  @ Thu, 13 Apr 2017 13:36:54:  26000000 
INFO  @ Thu, 13 Apr 2017 13:36:55:  27000000 
INFO  @ Thu, 13 Apr 2017 13:36:57:  28000000 
INFO  @ Thu, 13 Apr 2017 13:36:58:  29000000 
INFO  @ Thu, 13 Apr 2017 13:36:59:  30000000 
INFO  @ Thu, 13 Apr 2017 13:37:01:  31000000 
INFO  @ Thu, 13 Apr 2017 13:37:02:  32000000 
INFO  @ Thu, 13 Apr 2017 13:37:04:  33000000 
INFO  @ Thu, 13 Apr 2017 13:37:05:  34000000 
INFO  @ Thu, 13 Apr 2017 13:37:07:  35000000 
INFO  @ Thu, 13 Apr 2017 13:37:08:  36000000 
INFO  @ Thu, 13 Apr 2017 13:37:09:  37000000 
INFO  @ Thu, 13 Apr 2017 13:37:11:  38000000 
INFO  @ Thu, 13 Apr 2017 13:37:12:  39000000 
INFO  @ Thu, 13 Apr 2017 13:37:14:  40000000 
INFO  @ Thu, 13 Apr 2017 13:37:15:  41000000 
INFO  @ Thu, 13 Apr 2017 13:37:16:  42000000 
INFO  @ Thu, 13 Apr 2017 13:37:18:  43000000 
INFO  @ Thu, 13 Apr 2017 13:37:19:  44000000 
INFO  @ Thu, 13 Apr 2017 13:37:21:  45000000 
INFO  @ Thu, 13 Apr 2017 13:37:22:  46000000 
INFO  @ Thu, 13 Apr 2017 13:37:24:  47000000 
INFO  @ Thu, 13 Apr 2017 13:37:25:  48000000 
INFO  @ Thu, 13 Apr 2017 13:37:26:  49000000 
INFO  @ Thu, 13 Apr 2017 13:37:28:  50000000 
INFO  @ Thu, 13 Apr 2017 13:37:30: #1 tag size is determined as 49 bps 
INFO  @ Thu, 13 Apr 2017 13:37:30: #1 tag size = 49 
INFO  @ Thu, 13 Apr 2017 13:37:30: #1  total tags in treatment: 18384762 
INFO  @ Thu, 13 Apr 2017 13:37:30: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 13:37:30: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:37:30: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:37:30: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:37:30: #2 Use 145 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:37:30: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:37:30: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:37:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:41:06: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:41:06: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:41:06: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:41:06: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:41:06: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:46:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:46:30: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:46:32: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:46:33: Done! 
INFO  @ Thu, 13 Apr 2017 13:46:37: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:47:21: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:49:27: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 13:50:22: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 13:55:44: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 13:58:23: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:05:23: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:06:02: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:08:06: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:08:55: Values in your input bedGraph files will be multiplied by 18.384762 ... 
INFO  @ Thu, 13 Apr 2017 14:14:21: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 14:15:01: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:17:51: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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	46842

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

Start	2017-04-13 13:35:30
End	2017-04-13 13:47:14
Elapsed	00:11:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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--------------------
18772 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:35:49: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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 13:35:49: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:35:49: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:35:51:  1000000 
INFO  @ Thu, 13 Apr 2017 13:35:53:  2000000 
INFO  @ Thu, 13 Apr 2017 13:35:55:  3000000 
INFO  @ Thu, 13 Apr 2017 13:35:57:  4000000 
INFO  @ Thu, 13 Apr 2017 13:35:59:  5000000 
INFO  @ Thu, 13 Apr 2017 13:36:01:  6000000 
INFO  @ Thu, 13 Apr 2017 13:36:03:  7000000 
INFO  @ Thu, 13 Apr 2017 13:36:05:  8000000 
INFO  @ Thu, 13 Apr 2017 13:36:07:  9000000 
INFO  @ Thu, 13 Apr 2017 13:36:08: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:36:10:  1000000 
INFO  @ Thu, 13 Apr 2017 13:36:12:  2000000 
INFO  @ Thu, 13 Apr 2017 13:36:14:  3000000 
INFO  @ Thu, 13 Apr 2017 13:36:16:  4000000 
INFO  @ Thu, 13 Apr 2017 13:36:18:  5000000 
INFO  @ Thu, 13 Apr 2017 13:36:20:  6000000 
INFO  @ Thu, 13 Apr 2017 13:36:22:  7000000 
INFO  @ Thu, 13 Apr 2017 13:36:23:  8000000 
INFO  @ Thu, 13 Apr 2017 13:36:25:  9000000 
INFO  @ Thu, 13 Apr 2017 13:36:27:  10000000 
INFO  @ Thu, 13 Apr 2017 13:36:29:  11000000 
INFO  @ Thu, 13 Apr 2017 13:36:31:  12000000 
INFO  @ Thu, 13 Apr 2017 13:36:33:  13000000 
INFO  @ Thu, 13 Apr 2017 13:36:35:  14000000 
INFO  @ Thu, 13 Apr 2017 13:36:37:  15000000 
INFO  @ Thu, 13 Apr 2017 13:36:39:  16000000 
INFO  @ Thu, 13 Apr 2017 13:36:40:  17000000 
INFO  @ Thu, 13 Apr 2017 13:36:42:  18000000 
INFO  @ Thu, 13 Apr 2017 13:36:44:  19000000 
INFO  @ Thu, 13 Apr 2017 13:36:46:  20000000 
INFO  @ Thu, 13 Apr 2017 13:36:47:  21000000 
INFO  @ Thu, 13 Apr 2017 13:36:49:  22000000 
INFO  @ Thu, 13 Apr 2017 13:36:51:  23000000 
INFO  @ Thu, 13 Apr 2017 13:36:53:  24000000 
INFO  @ Thu, 13 Apr 2017 13:36:55:  25000000 
INFO  @ Thu, 13 Apr 2017 13:36:57:  26000000 
INFO  @ Thu, 13 Apr 2017 13:36:59:  27000000 
INFO  @ Thu, 13 Apr 2017 13:37:00:  28000000 
INFO  @ Thu, 13 Apr 2017 13:37:02:  29000000 
INFO  @ Thu, 13 Apr 2017 13:37:04:  30000000 
INFO  @ Thu, 13 Apr 2017 13:37:06:  31000000 
INFO  @ Thu, 13 Apr 2017 13:37:08:  32000000 
INFO  @ Thu, 13 Apr 2017 13:37:10:  33000000 
INFO  @ Thu, 13 Apr 2017 13:37:12:  34000000 
INFO  @ Thu, 13 Apr 2017 13:37:14:  35000000 
INFO  @ Thu, 13 Apr 2017 13:37:15:  36000000 
INFO  @ Thu, 13 Apr 2017 13:37:17:  37000000 
INFO  @ Thu, 13 Apr 2017 13:37:19:  38000000 
INFO  @ Thu, 13 Apr 2017 13:37:21:  39000000 
INFO  @ Thu, 13 Apr 2017 13:37:23:  40000000 
INFO  @ Thu, 13 Apr 2017 13:37:25:  41000000 
INFO  @ Thu, 13 Apr 2017 13:37:27:  42000000 
INFO  @ Thu, 13 Apr 2017 13:37:29:  43000000 
INFO  @ Thu, 13 Apr 2017 13:37:31:  44000000 
INFO  @ Thu, 13 Apr 2017 13:37:33:  45000000 
INFO  @ Thu, 13 Apr 2017 13:37:35:  46000000 
INFO  @ Thu, 13 Apr 2017 13:37:37:  47000000 
INFO  @ Thu, 13 Apr 2017 13:37:39:  48000000 
INFO  @ Thu, 13 Apr 2017 13:37:41:  49000000 
INFO  @ Thu, 13 Apr 2017 13:37:43:  50000000 
INFO  @ Thu, 13 Apr 2017 13:37:45: #1 tag size is determined as 50 bps 
INFO  @ Thu, 13 Apr 2017 13:37:45: #1 tag size = 50 
INFO  @ Thu, 13 Apr 2017 13:37:45: #1  total tags in treatment: 9192381 
INFO  @ Thu, 13 Apr 2017 13:37:45: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 13:37:45: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:37:45: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:37:45: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:37:45: #2 Use 145 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:37:45: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:37:45: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:37:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:40:57: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:40:57: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:40:57: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:40:57: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:40:57: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:47:04: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:47:07: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:47:08: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:47:10: 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	46843

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

Start	2017-04-13 13:35:31
End	2017-04-13 13:44:49
Elapsed	00:09:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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--------------------
5756 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:35:48: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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 13:35:48: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:35:48: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:35:50:  1000000 
INFO  @ Thu, 13 Apr 2017 13:35:52:  2000000 
INFO  @ Thu, 13 Apr 2017 13:35:53:  3000000 
INFO  @ Thu, 13 Apr 2017 13:35:56:  4000000 
INFO  @ Thu, 13 Apr 2017 13:35:57:  5000000 
INFO  @ Thu, 13 Apr 2017 13:35:59:  6000000 
INFO  @ Thu, 13 Apr 2017 13:36:00:  7000000 
INFO  @ Thu, 13 Apr 2017 13:36:02:  8000000 
INFO  @ Thu, 13 Apr 2017 13:36:04:  9000000 
INFO  @ Thu, 13 Apr 2017 13:36:05: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:36:06:  1000000 
INFO  @ Thu, 13 Apr 2017 13:36:07:  2000000 
INFO  @ Thu, 13 Apr 2017 13:36:09:  3000000 
INFO  @ Thu, 13 Apr 2017 13:36:10:  4000000 
INFO  @ Thu, 13 Apr 2017 13:36:12:  5000000 
INFO  @ Thu, 13 Apr 2017 13:36:13:  6000000 
INFO  @ Thu, 13 Apr 2017 13:36:15:  7000000 
INFO  @ Thu, 13 Apr 2017 13:36:16:  8000000 
INFO  @ Thu, 13 Apr 2017 13:36:18:  9000000 
INFO  @ Thu, 13 Apr 2017 13:36:19:  10000000 
INFO  @ Thu, 13 Apr 2017 13:36:21:  11000000 
INFO  @ Thu, 13 Apr 2017 13:36:22:  12000000 
INFO  @ Thu, 13 Apr 2017 13:36:23:  13000000 
INFO  @ Thu, 13 Apr 2017 13:36:25:  14000000 
INFO  @ Thu, 13 Apr 2017 13:36:26:  15000000 
INFO  @ Thu, 13 Apr 2017 13:36:28:  16000000 
INFO  @ Thu, 13 Apr 2017 13:36:29:  17000000 
INFO  @ Thu, 13 Apr 2017 13:36:31:  18000000 
INFO  @ Thu, 13 Apr 2017 13:36:32:  19000000 
INFO  @ Thu, 13 Apr 2017 13:36:34:  20000000 
INFO  @ Thu, 13 Apr 2017 13:36:35:  21000000 
INFO  @ Thu, 13 Apr 2017 13:36:37:  22000000 
INFO  @ Thu, 13 Apr 2017 13:36:38:  23000000 
INFO  @ Thu, 13 Apr 2017 13:36:39:  24000000 
INFO  @ Thu, 13 Apr 2017 13:36:41:  25000000 
INFO  @ Thu, 13 Apr 2017 13:36:42:  26000000 
INFO  @ Thu, 13 Apr 2017 13:36:44:  27000000 
INFO  @ Thu, 13 Apr 2017 13:36:45:  28000000 
INFO  @ Thu, 13 Apr 2017 13:36:47:  29000000 
INFO  @ Thu, 13 Apr 2017 13:36:48:  30000000 
INFO  @ Thu, 13 Apr 2017 13:36:50:  31000000 
INFO  @ Thu, 13 Apr 2017 13:36:51:  32000000 
INFO  @ Thu, 13 Apr 2017 13:36:52:  33000000 
INFO  @ Thu, 13 Apr 2017 13:36:54:  34000000 
INFO  @ Thu, 13 Apr 2017 13:36:55:  35000000 
INFO  @ Thu, 13 Apr 2017 13:36:57:  36000000 
INFO  @ Thu, 13 Apr 2017 13:36:58:  37000000 
INFO  @ Thu, 13 Apr 2017 13:37:00:  38000000 
INFO  @ Thu, 13 Apr 2017 13:37:01:  39000000 
INFO  @ Thu, 13 Apr 2017 13:37:03:  40000000 
INFO  @ Thu, 13 Apr 2017 13:37:04:  41000000 
INFO  @ Thu, 13 Apr 2017 13:37:06:  42000000 
INFO  @ Thu, 13 Apr 2017 13:37:07:  43000000 
INFO  @ Thu, 13 Apr 2017 13:37:08:  44000000 
INFO  @ Thu, 13 Apr 2017 13:37:10:  45000000 
INFO  @ Thu, 13 Apr 2017 13:37:11:  46000000 
INFO  @ Thu, 13 Apr 2017 13:37:13:  47000000 
INFO  @ Thu, 13 Apr 2017 13:37:14:  48000000 
INFO  @ Thu, 13 Apr 2017 13:37:16:  49000000 
INFO  @ Thu, 13 Apr 2017 13:37:17:  50000000 
INFO  @ Thu, 13 Apr 2017 13:37:19: #1 tag size is determined as 50 bps 
INFO  @ Thu, 13 Apr 2017 13:37:19: #1 tag size = 50 
INFO  @ Thu, 13 Apr 2017 13:37:19: #1  total tags in treatment: 9192381 
INFO  @ Thu, 13 Apr 2017 13:37:19: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 13:37:19: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:37:19: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:37:19: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:37:19: #2 Use 145 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:37:19: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:37:19: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:37:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:39:53: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:39:53: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:39:53: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:39:53: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:39:53: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:44:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:44:45: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:44:46: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:44:46: Done!

Num	4
ID	task.callpeak_naive_overlap.naive_overlap.line_59.id_13
Name	naive_overlap
Thread	thread_Root
PID	46886

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

Start	2017-04-13 14:26:34
End	2017-04-13 14:27:45
Elapsed	00:01:11
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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--------------------
51055 (process ID) old priority 0, new priority 19
Waiting for 54 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	173442	173987	Peak_5414	505	.	21.27987	50.51068	46.91261	153

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	173442	173987	Peak_5414	505	.	21.27987	50.51068	46.91261	153

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270853.1	1984464	1985293	Peak_8770	347	.	17.40685	34.78276	31.45039	535

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270853.1	1984464	1985293	Peak_8770	347	.	17.40685	34.78276	31.45039	535

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	137513	137812	Peak_42714	138	.	8.05100	13.81212	11.29985	102

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	137513	137812	Peak_42714	138	.	8.05100	13.81212	11.29985	102

Num	5
ID	task.callpeak_idr.idr2_rep1_pr.line_74.id_14
Name	idr2 rep1-pr
Thread	thread_Root
PID	46887

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

Start	2017-04-13 14:27:47
End	2017-04-13 14:34:05
Elapsed	00:06:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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--------------------
51773 (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	26480

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

Start	2017-04-13 14:34:06
End	2017-04-13 14:34:06
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_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	26485

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

Start	2017-04-13 14:34:06
End	2017-04-13 14:34:06
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_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	26499

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

Start	2017-04-13 14:34:06
End	2017-04-13 14:34:06
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_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	26511

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

Start	2017-04-13 14:34:06
End	2017-04-13 14:34:06
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_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	46889

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

Start	2017-04-13 14:34:08
End	2017-04-13 14:35:30
Elapsed	00:01:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/qc/ZNF467_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/ZNF467_MACS2/out/qc/ZNF467_MACS2_IDR_final.qc

# SYS command. line 288

 echo -e "0\t34254	0	""0\t34254\t34254\tself_pseudo_rep_rep1\tself_pseudo_rep_rep1\t0.0\t1.0\tpass" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/qc/ZNF467_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--------------------
55770 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

Num	11
ID	task.callpeak_idr.FRiP_rep1_pr.line_120.id_22
Name	FRiP rep1-pr
Thread	thread_Root
PID	46890

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

Start	2017-04-13 14:34:08
End	2017-04-13 14:35:31
Elapsed	00:01:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -s -l -73 -r 73 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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--------------------
55771 (process ID) old priority 0, new priority 19
Waiting for 5 seconds.

 
--------------------Stderr--------------------
***** WARNING: File stdin has inconsistent naming convention for record:
GL000008.2	302	352	N	1000	+

***** WARNING: File stdin has inconsistent naming convention for record:
GL000008.2	302	352	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	29923

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

Start	2017-04-13 14:35:33
End	2017-04-13 14:36:41
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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--------------------
29927 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196484.1	173444	173978	Peak_7254	741	.	23.19326	74.15192	70.74121	139

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196484.1	173444	173978	Peak_7254	741	.	23.19326	74.15192	70.74121	139

Num	13
ID	task.report.peak2hammock.line_361.id_26
Name	peak2hammock
Thread	thread_Root
PID	33016

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

Start	2017-04-13 14:36:42
End	2017-04-13 14:36:52
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
33021 (process ID) old priority 0, new priority 19

Num	14
ID	task.report.peak2hammock.line_361.id_27
Name	peak2hammock
Thread	thread_Root
PID	33528

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

Start	2017-04-13 14:36:53
End	2017-04-13 14:37:01
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/optimal_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
33532 (process ID) old priority 0, new priority 19

Num	15
ID	task.report.peak2hammock.line_361.id_28
Name	peak2hammock
Thread	thread_Root
PID	34083

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

Start	2017-04-13 14:37:02
End	2017-04-13 14:37:11
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/conservative_set/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
34087 (process ID) old priority 0, new priority 19

Num	16
ID	task.report.peak2hammock.line_361.id_29
Name	peak2hammock
Thread	thread_Root
PID	34538

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

Start	2017-04-13 14:37:12
End	2017-04-13 14:37:24
Elapsed	00:00:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_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/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZNF467_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
34542 (process ID) old priority 0, new priority 19

Num	17
ID	task.graphviz.report.line_97.id_30
Name	report
Thread	thread_Root
PID	35142

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

Start	2017-04-13 14:37:25
End	2017-04-13 14:37:33
Elapsed	00:00:08
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/ZNF467_MACS2/out/report/ZNF467_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/report/ZNF467_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/report/ZNF467_MACS2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
35146 (process ID) old priority 0, new priority 19

Num	18
ID	task.report.pdf2png.line_328.id_31
Name	pdf2png
Thread	thread_Root
PID	35160

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

Start	2017-04-13 14:37:25
End	2017-04-13 14:37:36
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/qc/rep1/SRR1370886_1.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/qc/rep1/SRR1370886_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/ZNF467_MACS2/out/qc/rep1/SRR1370886_1.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/qc/rep1/SRR1370886_1.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
35164 (process ID) old priority 0, new priority 19

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, ZNF467_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF467_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_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/ZNF467_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	4870.ZNF467_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