| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 19493 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:55 | | End | 2016-12-21 14:14:55 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/signal/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/signal/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
| | Dependencies | | |
# SYS command. line 69
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 70
export LC_COLLATE=C
# SYS command. line 75
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 88
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
# SYS command. line 92
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_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 111
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1 -o "SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_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/ZNF621/out/signal/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
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 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1 -o "SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_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/ZNF621/out/signal/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg
# SYS command. line 143
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
12702 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Thu, 22 Dec 2016 02:49:14:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_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, 22 Dec 2016 02:49:14: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:49:14: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:49:16: 1000000
INFO @ Thu, 22 Dec 2016 02:49:18: 2000000
INFO @ Thu, 22 Dec 2016 02:49:20: 3000000
INFO @ Thu, 22 Dec 2016 02:49:21: 4000000
INFO @ Thu, 22 Dec 2016 02:49:23: 5000000
INFO @ Thu, 22 Dec 2016 02:49:24: 6000000
INFO @ Thu, 22 Dec 2016 02:49:26: 7000000
INFO @ Thu, 22 Dec 2016 02:49:28: 8000000
INFO @ Thu, 22 Dec 2016 02:49:29: 9000000
INFO @ Thu, 22 Dec 2016 02:49:31: 10000000
INFO @ Thu, 22 Dec 2016 02:49:33: 11000000
INFO @ Thu, 22 Dec 2016 02:49:34: 12000000
INFO @ Thu, 22 Dec 2016 02:49:36: 13000000
INFO @ Thu, 22 Dec 2016 02:49:36: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:49:38: 1000000
INFO @ Thu, 22 Dec 2016 02:49:40: 2000000
INFO @ Thu, 22 Dec 2016 02:49:42: 3000000
INFO @ Thu, 22 Dec 2016 02:49:43: 4000000
INFO @ Thu, 22 Dec 2016 02:49:45: 5000000
INFO @ Thu, 22 Dec 2016 02:49:47: 6000000
INFO @ Thu, 22 Dec 2016 02:49:48: 7000000
INFO @ Thu, 22 Dec 2016 02:49:50: 8000000
INFO @ Thu, 22 Dec 2016 02:49:52: 9000000
INFO @ Thu, 22 Dec 2016 02:49:53: 10000000
INFO @ Thu, 22 Dec 2016 02:49:55: 11000000
INFO @ Thu, 22 Dec 2016 02:49:57: 12000000
INFO @ Thu, 22 Dec 2016 02:49:58: 13000000
INFO @ Thu, 22 Dec 2016 02:50:00: 14000000
INFO @ Thu, 22 Dec 2016 02:50:02: 15000000
INFO @ Thu, 22 Dec 2016 02:50:03: 16000000
INFO @ Thu, 22 Dec 2016 02:50:05: 17000000
INFO @ Thu, 22 Dec 2016 02:50:07: 18000000
INFO @ Thu, 22 Dec 2016 02:50:08: 19000000
INFO @ Thu, 22 Dec 2016 02:50:10: 20000000
INFO @ Thu, 22 Dec 2016 02:50:12: 21000000
INFO @ Thu, 22 Dec 2016 02:50:13: 22000000
INFO @ Thu, 22 Dec 2016 02:50:15: 23000000
INFO @ Thu, 22 Dec 2016 02:50:17: 24000000
INFO @ Thu, 22 Dec 2016 02:50:18: 25000000
INFO @ Thu, 22 Dec 2016 02:50:20: 26000000
INFO @ Thu, 22 Dec 2016 02:50:22: 27000000
INFO @ Thu, 22 Dec 2016 02:50:23: 28000000
INFO @ Thu, 22 Dec 2016 02:50:25: 29000000
INFO @ Thu, 22 Dec 2016 02:50:27: 30000000
INFO @ Thu, 22 Dec 2016 02:50:28: 31000000
INFO @ Thu, 22 Dec 2016 02:50:30: 32000000
INFO @ Thu, 22 Dec 2016 02:50:32: 33000000
INFO @ Thu, 22 Dec 2016 02:50:33: 34000000
INFO @ Thu, 22 Dec 2016 02:50:35: 35000000
INFO @ Thu, 22 Dec 2016 02:50:37: 36000000
INFO @ Thu, 22 Dec 2016 02:50:39: 37000000
INFO @ Thu, 22 Dec 2016 02:50:40: 38000000
INFO @ Thu, 22 Dec 2016 02:50:42: 39000000
INFO @ Thu, 22 Dec 2016 02:50:44: 40000000
INFO @ Thu, 22 Dec 2016 02:50:45: 41000000
INFO @ Thu, 22 Dec 2016 02:50:47: 42000000
INFO @ Thu, 22 Dec 2016 02:50:49: 43000000
INFO @ Thu, 22 Dec 2016 02:50:50: 44000000
INFO @ Thu, 22 Dec 2016 02:50:52: 45000000
INFO @ Thu, 22 Dec 2016 02:50:53: 46000000
INFO @ Thu, 22 Dec 2016 02:50:55: 47000000
INFO @ Thu, 22 Dec 2016 02:50:57: 48000000
INFO @ Thu, 22 Dec 2016 02:50:58: 49000000
INFO @ Thu, 22 Dec 2016 02:51:00: 50000000
INFO @ Thu, 22 Dec 2016 02:51:02: #1 tag size is determined as 69 bps
INFO @ Thu, 22 Dec 2016 02:51:02: #1 tag size = 69
INFO @ Thu, 22 Dec 2016 02:51:02: #1 total tags in treatment: 13139204
INFO @ Thu, 22 Dec 2016 02:51:02: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:51:02: #1 finished!
INFO @ Thu, 22 Dec 2016 02:51:02: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:51:02: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:51:02: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 02:51:02: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:51:02: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 02:51:02: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:54:57: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 02:54:57: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 02:54:57: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 02:54:57: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 02:54:57: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:01:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:01:11: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 03:01:12: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 03:01:13: Done!
INFO @ Thu, 22 Dec 2016 03:01:18:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_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/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/rep1/SRR1370911_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 for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Thu, 22 Dec 2016 03:01:18: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:01:18: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:01:20: 1000000
INFO @ Thu, 22 Dec 2016 03:01:22: 2000000
INFO @ Thu, 22 Dec 2016 03:01:23: 3000000
INFO @ Thu, 22 Dec 2016 03:01:25: 4000000
INFO @ Thu, 22 Dec 2016 03:01:26: 5000000
INFO @ Thu, 22 Dec 2016 03:01:28: 6000000
INFO @ Thu, 22 Dec 2016 03:01:29: 7000000
INFO @ Thu, 22 Dec 2016 03:01:31: 8000000
INFO @ Thu, 22 Dec 2016 03:01:32: 9000000
INFO @ Thu, 22 Dec 2016 03:01:34: 10000000
INFO @ Thu, 22 Dec 2016 03:01:36: 11000000
INFO @ Thu, 22 Dec 2016 03:01:37: 12000000
INFO @ Thu, 22 Dec 2016 03:01:39: 13000000
INFO @ Thu, 22 Dec 2016 03:01:39: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:01:41: 1000000
INFO @ Thu, 22 Dec 2016 03:01:42: 2000000
INFO @ Thu, 22 Dec 2016 03:01:44: 3000000
INFO @ Thu, 22 Dec 2016 03:01:45: 4000000
INFO @ Thu, 22 Dec 2016 03:01:47: 5000000
INFO @ Thu, 22 Dec 2016 03:01:49: 6000000
INFO @ Thu, 22 Dec 2016 03:01:50: 7000000
INFO @ Thu, 22 Dec 2016 03:01:52: 8000000
INFO @ Thu, 22 Dec 2016 03:01:53: 9000000
INFO @ Thu, 22 Dec 2016 03:01:55: 10000000
INFO @ Thu, 22 Dec 2016 03:01:56: 11000000
INFO @ Thu, 22 Dec 2016 03:01:58: 12000000
INFO @ Thu, 22 Dec 2016 03:02:00: 13000000
INFO @ Thu, 22 Dec 2016 03:02:01: 14000000
INFO @ Thu, 22 Dec 2016 03:02:03: 15000000
INFO @ Thu, 22 Dec 2016 03:02:05: 16000000
INFO @ Thu, 22 Dec 2016 03:02:06: 17000000
INFO @ Thu, 22 Dec 2016 03:02:08: 18000000
INFO @ Thu, 22 Dec 2016 03:02:10: 19000000
INFO @ Thu, 22 Dec 2016 03:02:11: 20000000
INFO @ Thu, 22 Dec 2016 03:02:13: 21000000
INFO @ Thu, 22 Dec 2016 03:02:14: 22000000
INFO @ Thu, 22 Dec 2016 03:02:16: 23000000
INFO @ Thu, 22 Dec 2016 03:02:18: 24000000
INFO @ Thu, 22 Dec 2016 03:02:19: 25000000
INFO @ Thu, 22 Dec 2016 03:02:21: 26000000
INFO @ Thu, 22 Dec 2016 03:02:23: 27000000
INFO @ Thu, 22 Dec 2016 03:02:24: 28000000
INFO @ Thu, 22 Dec 2016 03:02:26: 29000000
INFO @ Thu, 22 Dec 2016 03:02:27: 30000000
INFO @ Thu, 22 Dec 2016 03:02:29: 31000000
INFO @ Thu, 22 Dec 2016 03:02:31: 32000000
INFO @ Thu, 22 Dec 2016 03:02:32: 33000000
INFO @ Thu, 22 Dec 2016 03:02:34: 34000000
INFO @ Thu, 22 Dec 2016 03:02:36: 35000000
INFO @ Thu, 22 Dec 2016 03:02:37: 36000000
INFO @ Thu, 22 Dec 2016 03:02:39: 37000000
INFO @ Thu, 22 Dec 2016 03:02:41: 38000000
INFO @ Thu, 22 Dec 2016 03:02:42: 39000000
INFO @ Thu, 22 Dec 2016 03:02:44: 40000000
INFO @ Thu, 22 Dec 2016 03:02:46: 41000000
INFO @ Thu, 22 Dec 2016 03:02:47: 42000000
INFO @ Thu, 22 Dec 2016 03:02:49: 43000000
INFO @ Thu, 22 Dec 2016 03:02:50: 44000000
INFO @ Thu, 22 Dec 2016 03:02:52: 45000000
INFO @ Thu, 22 Dec 2016 03:02:54: 46000000
INFO @ Thu, 22 Dec 2016 03:02:55: 47000000
INFO @ Thu, 22 Dec 2016 03:02:57: 48000000
INFO @ Thu, 22 Dec 2016 03:02:58: 49000000
INFO @ Thu, 22 Dec 2016 03:03:00: 50000000
INFO @ Thu, 22 Dec 2016 03:03:02: #1 tag size is determined as 69 bps
INFO @ Thu, 22 Dec 2016 03:03:02: #1 tag size = 69
INFO @ Thu, 22 Dec 2016 03:03:02: #1 total tags in treatment: 13139204
INFO @ Thu, 22 Dec 2016 03:03:02: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:03:02: #1 finished!
INFO @ Thu, 22 Dec 2016 03:03:02: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:03:02: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:03:02: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 03:03:02: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:03:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 03:03:02: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:07:46: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:11:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:11:26: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 03:11:31: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 03:11:35: Done!
INFO @ Thu, 22 Dec 2016 03:11:58: Read and build treatment bedGraph...
INFO @ Thu, 22 Dec 2016 03:12:27: Read and build control bedGraph...
INFO @ Thu, 22 Dec 2016 03:14:20: Build scoreTrackII...
INFO @ Thu, 22 Dec 2016 03:15:56: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 22 Dec 2016 03:21:38: Write bedGraph of scores...
INFO @ Thu, 22 Dec 2016 03:24:14: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/rep1/SRR1370911_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'!
Chromosome KN196487.1 isn't in /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes line 1 of stdin
--------------------Post mortem info--------------------
==============================================================
job_number: 19493
submission_time: Wed Dec 21 14:14:55 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /software/samtools/samtools-1.2/bin:/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
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/chipseq.bds.20161221_141448_010/task.callpeak_macs2.macs2_rep1.line_67.id_10.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/chipseq.bds.20161221_141448_010/task.callpeak_macs2.macs2_rep1.line_67.id_10.stdout.cluster
jobshare: 0
env_list: C_INCLUDE_PATH=/software/samtools/samtools-1.2/include/htslib,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 32898 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,SAMTOOLS_HOME=/software/samtools/samtools-1.2/bin,SSH_TTY=/dev/pts/4,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=9035,TERM=screen,SGE_ROOT=/var/lib/gridengine,PATH=/software/samtools/samtools-1.2/bin:/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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=51233.ZNF621.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_cTVn8v,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:samtools/1.2,SSH_CONNECTION=171.65.77.8 32898 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MANPATH=/software/samtools/samtools-1.2/share/man:/usr/share/man,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
scheduling info: queue instance "q@kali" dropped because it is temporarily not available
queue instance "q@surya" dropped because it is disabled
queue instance "amd.q@wotan" dropped because it is full
queue instance "q@nandi" dropped because it is full
queue instance "q@kadru" dropped because it is full
All queues dropped because of overload or full
|
| Num | 2 | | ID | task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 | | Name | macs2 rep1-pr1 | | Thread | thread_Root | | PID | 19497 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:58 | | End | 2016-12-22 04:03:01 | | Elapsed | 13:48:02 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
| | Dependencies | | |
# SYS command. line 69
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 70
export LC_COLLATE=C
# SYS command. line 75
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 88
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
# SYS command. line 92
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 111
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
controlReads=$(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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg
# SYS command. line 143
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
13641 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Thu, 22 Dec 2016 03:35:31:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_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, 22 Dec 2016 03:35:31: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:35:31: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:35:33: 1000000
INFO @ Thu, 22 Dec 2016 03:35:35: 2000000
INFO @ Thu, 22 Dec 2016 03:35:37: 3000000
INFO @ Thu, 22 Dec 2016 03:35:38: 4000000
INFO @ Thu, 22 Dec 2016 03:35:40: 5000000
INFO @ Thu, 22 Dec 2016 03:35:41: 6000000
INFO @ Thu, 22 Dec 2016 03:35:43: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:35:44: 1000000
INFO @ Thu, 22 Dec 2016 03:35:46: 2000000
INFO @ Thu, 22 Dec 2016 03:35:48: 3000000
INFO @ Thu, 22 Dec 2016 03:35:49: 4000000
INFO @ Thu, 22 Dec 2016 03:35:51: 5000000
INFO @ Thu, 22 Dec 2016 03:35:53: 6000000
INFO @ Thu, 22 Dec 2016 03:35:54: 7000000
INFO @ Thu, 22 Dec 2016 03:35:56: 8000000
INFO @ Thu, 22 Dec 2016 03:35:57: 9000000
INFO @ Thu, 22 Dec 2016 03:35:59: 10000000
INFO @ Thu, 22 Dec 2016 03:36:01: 11000000
INFO @ Thu, 22 Dec 2016 03:36:02: 12000000
INFO @ Thu, 22 Dec 2016 03:36:04: 13000000
INFO @ Thu, 22 Dec 2016 03:36:06: 14000000
INFO @ Thu, 22 Dec 2016 03:36:07: 15000000
INFO @ Thu, 22 Dec 2016 03:36:09: 16000000
INFO @ Thu, 22 Dec 2016 03:36:11: 17000000
INFO @ Thu, 22 Dec 2016 03:36:12: 18000000
INFO @ Thu, 22 Dec 2016 03:36:14: 19000000
INFO @ Thu, 22 Dec 2016 03:36:15: 20000000
INFO @ Thu, 22 Dec 2016 03:36:17: 21000000
INFO @ Thu, 22 Dec 2016 03:36:19: 22000000
INFO @ Thu, 22 Dec 2016 03:36:20: 23000000
INFO @ Thu, 22 Dec 2016 03:36:22: 24000000
INFO @ Thu, 22 Dec 2016 03:36:24: 25000000
INFO @ Thu, 22 Dec 2016 03:36:25: 26000000
INFO @ Thu, 22 Dec 2016 03:36:27: 27000000
INFO @ Thu, 22 Dec 2016 03:36:28: 28000000
INFO @ Thu, 22 Dec 2016 03:36:30: 29000000
INFO @ Thu, 22 Dec 2016 03:36:32: 30000000
INFO @ Thu, 22 Dec 2016 03:36:33: 31000000
INFO @ Thu, 22 Dec 2016 03:36:35: 32000000
INFO @ Thu, 22 Dec 2016 03:36:37: 33000000
INFO @ Thu, 22 Dec 2016 03:36:38: 34000000
INFO @ Thu, 22 Dec 2016 03:36:40: 35000000
INFO @ Thu, 22 Dec 2016 03:36:42: 36000000
INFO @ Thu, 22 Dec 2016 03:36:43: 37000000
INFO @ Thu, 22 Dec 2016 03:36:45: 38000000
INFO @ Thu, 22 Dec 2016 03:36:47: 39000000
INFO @ Thu, 22 Dec 2016 03:36:48: 40000000
INFO @ Thu, 22 Dec 2016 03:36:50: 41000000
INFO @ Thu, 22 Dec 2016 03:36:52: 42000000
INFO @ Thu, 22 Dec 2016 03:36:53: 43000000
INFO @ Thu, 22 Dec 2016 03:36:55: 44000000
INFO @ Thu, 22 Dec 2016 03:36:57: 45000000
INFO @ Thu, 22 Dec 2016 03:36:58: 46000000
INFO @ Thu, 22 Dec 2016 03:37:00: 47000000
INFO @ Thu, 22 Dec 2016 03:37:01: 48000000
INFO @ Thu, 22 Dec 2016 03:37:03: 49000000
INFO @ Thu, 22 Dec 2016 03:37:05: 50000000
INFO @ Thu, 22 Dec 2016 03:37:06: #1 tag size is determined as 69 bps
INFO @ Thu, 22 Dec 2016 03:37:06: #1 tag size = 69
INFO @ Thu, 22 Dec 2016 03:37:06: #1 total tags in treatment: 6569602
INFO @ Thu, 22 Dec 2016 03:37:06: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:37:06: #1 finished!
INFO @ Thu, 22 Dec 2016 03:37:06: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:37:06: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:37:06: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 03:37:06: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:37:06: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 03:37:06: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:44:32: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 03:44:32: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 03:44:32: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 03:44:32: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 03:44:32: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:51:51: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:51:52: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 03:51:53: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 03:51:54: Done!
INFO @ Thu, 22 Dec 2016 03:52:00:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr1/SRR1370911_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 for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Thu, 22 Dec 2016 03:52:00: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:52:00: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:52:02: 1000000
INFO @ Thu, 22 Dec 2016 03:52:03: 2000000
INFO @ Thu, 22 Dec 2016 03:52:05: 3000000
INFO @ Thu, 22 Dec 2016 03:52:07: 4000000
INFO @ Thu, 22 Dec 2016 03:52:09: 5000000
INFO @ Thu, 22 Dec 2016 03:52:10: 6000000
INFO @ Thu, 22 Dec 2016 03:52:12: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:52:13: 1000000
INFO @ Thu, 22 Dec 2016 03:52:15: 2000000
INFO @ Thu, 22 Dec 2016 03:52:17: 3000000
INFO @ Thu, 22 Dec 2016 03:52:18: 4000000
INFO @ Thu, 22 Dec 2016 03:52:20: 5000000
INFO @ Thu, 22 Dec 2016 03:52:22: 6000000
INFO @ Thu, 22 Dec 2016 03:52:23: 7000000
INFO @ Thu, 22 Dec 2016 03:52:25: 8000000
INFO @ Thu, 22 Dec 2016 03:52:26: 9000000
INFO @ Thu, 22 Dec 2016 03:52:28: 10000000
INFO @ Thu, 22 Dec 2016 03:52:30: 11000000
INFO @ Thu, 22 Dec 2016 03:52:31: 12000000
INFO @ Thu, 22 Dec 2016 03:52:33: 13000000
INFO @ Thu, 22 Dec 2016 03:52:35: 14000000
INFO @ Thu, 22 Dec 2016 03:52:36: 15000000
INFO @ Thu, 22 Dec 2016 03:52:38: 16000000
INFO @ Thu, 22 Dec 2016 03:52:40: 17000000
INFO @ Thu, 22 Dec 2016 03:52:41: 18000000
INFO @ Thu, 22 Dec 2016 03:52:43: 19000000
INFO @ Thu, 22 Dec 2016 03:52:45: 20000000
INFO @ Thu, 22 Dec 2016 03:52:46: 21000000
INFO @ Thu, 22 Dec 2016 03:52:48: 22000000
INFO @ Thu, 22 Dec 2016 03:52:50: 23000000
INFO @ Thu, 22 Dec 2016 03:52:51: 24000000
INFO @ Thu, 22 Dec 2016 03:52:53: 25000000
INFO @ Thu, 22 Dec 2016 03:52:54: 26000000
INFO @ Thu, 22 Dec 2016 03:52:56: 27000000
INFO @ Thu, 22 Dec 2016 03:52:58: 28000000
INFO @ Thu, 22 Dec 2016 03:52:59: 29000000
INFO @ Thu, 22 Dec 2016 03:53:01: 30000000
INFO @ Thu, 22 Dec 2016 03:53:03: 31000000
INFO @ Thu, 22 Dec 2016 03:53:04: 32000000
INFO @ Thu, 22 Dec 2016 03:53:06: 33000000
INFO @ Thu, 22 Dec 2016 03:53:07: 34000000
INFO @ Thu, 22 Dec 2016 03:53:09: 35000000
INFO @ Thu, 22 Dec 2016 03:53:11: 36000000
INFO @ Thu, 22 Dec 2016 03:53:12: 37000000
INFO @ Thu, 22 Dec 2016 03:53:14: 38000000
INFO @ Thu, 22 Dec 2016 03:53:16: 39000000
INFO @ Thu, 22 Dec 2016 03:53:17: 40000000
INFO @ Thu, 22 Dec 2016 03:53:19: 41000000
INFO @ Thu, 22 Dec 2016 03:53:20: 42000000
INFO @ Thu, 22 Dec 2016 03:53:22: 43000000
INFO @ Thu, 22 Dec 2016 03:53:24: 44000000
INFO @ Thu, 22 Dec 2016 03:53:25: 45000000
INFO @ Thu, 22 Dec 2016 03:53:27: 46000000
INFO @ Thu, 22 Dec 2016 03:53:29: 47000000
INFO @ Thu, 22 Dec 2016 03:53:30: 48000000
INFO @ Thu, 22 Dec 2016 03:53:32: 49000000
INFO @ Thu, 22 Dec 2016 03:53:33: 50000000
INFO @ Thu, 22 Dec 2016 03:53:35: #1 tag size is determined as 69 bps
INFO @ Thu, 22 Dec 2016 03:53:35: #1 tag size = 69
INFO @ Thu, 22 Dec 2016 03:53:35: #1 total tags in treatment: 6569602
INFO @ Thu, 22 Dec 2016 03:53:35: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:53:35: #1 finished!
INFO @ Thu, 22 Dec 2016 03:53:35: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:53:35: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:53:35: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 03:53:35: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:53:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 03:53:35: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:58:23: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:02:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:02:30: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 04:02:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370911_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 04:02:40: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 19499 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:59 | | End | 2016-12-22 04:24:53 | | Elapsed | 14:09:53 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
| | Dependencies | | |
# SYS command. line 69
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 70
export LC_COLLATE=C
# SYS command. line 75
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 88
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
# SYS command. line 92
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 111
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
controlReads=$(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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg
# SYS command. line 143
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
13987 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Thu, 22 Dec 2016 03:56:15:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_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, 22 Dec 2016 03:56:15: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:56:15: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:56:17: 1000000
INFO @ Thu, 22 Dec 2016 03:56:19: 2000000
INFO @ Thu, 22 Dec 2016 03:56:21: 3000000
INFO @ Thu, 22 Dec 2016 03:56:22: 4000000
INFO @ Thu, 22 Dec 2016 03:56:24: 5000000
INFO @ Thu, 22 Dec 2016 03:56:26: 6000000
INFO @ Thu, 22 Dec 2016 03:56:27: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:56:29: 1000000
INFO @ Thu, 22 Dec 2016 03:56:31: 2000000
INFO @ Thu, 22 Dec 2016 03:56:33: 3000000
INFO @ Thu, 22 Dec 2016 03:56:34: 4000000
INFO @ Thu, 22 Dec 2016 03:56:36: 5000000
INFO @ Thu, 22 Dec 2016 03:56:38: 6000000
INFO @ Thu, 22 Dec 2016 03:56:39: 7000000
INFO @ Thu, 22 Dec 2016 03:56:41: 8000000
INFO @ Thu, 22 Dec 2016 03:56:43: 9000000
INFO @ Thu, 22 Dec 2016 03:56:44: 10000000
INFO @ Thu, 22 Dec 2016 03:56:46: 11000000
INFO @ Thu, 22 Dec 2016 03:56:48: 12000000
INFO @ Thu, 22 Dec 2016 03:56:49: 13000000
INFO @ Thu, 22 Dec 2016 03:56:51: 14000000
INFO @ Thu, 22 Dec 2016 03:56:53: 15000000
INFO @ Thu, 22 Dec 2016 03:56:55: 16000000
INFO @ Thu, 22 Dec 2016 03:56:56: 17000000
INFO @ Thu, 22 Dec 2016 03:56:58: 18000000
INFO @ Thu, 22 Dec 2016 03:57:00: 19000000
INFO @ Thu, 22 Dec 2016 03:57:01: 20000000
INFO @ Thu, 22 Dec 2016 03:57:03: 21000000
INFO @ Thu, 22 Dec 2016 03:57:05: 22000000
INFO @ Thu, 22 Dec 2016 03:57:06: 23000000
INFO @ Thu, 22 Dec 2016 03:57:08: 24000000
INFO @ Thu, 22 Dec 2016 03:57:10: 25000000
INFO @ Thu, 22 Dec 2016 03:57:12: 26000000
INFO @ Thu, 22 Dec 2016 03:57:13: 27000000
INFO @ Thu, 22 Dec 2016 03:57:15: 28000000
INFO @ Thu, 22 Dec 2016 03:57:17: 29000000
INFO @ Thu, 22 Dec 2016 03:57:18: 30000000
INFO @ Thu, 22 Dec 2016 03:57:20: 31000000
INFO @ Thu, 22 Dec 2016 03:57:22: 32000000
INFO @ Thu, 22 Dec 2016 03:57:23: 33000000
INFO @ Thu, 22 Dec 2016 03:57:25: 34000000
INFO @ Thu, 22 Dec 2016 03:57:27: 35000000
INFO @ Thu, 22 Dec 2016 03:57:29: 36000000
INFO @ Thu, 22 Dec 2016 03:57:31: 37000000
INFO @ Thu, 22 Dec 2016 03:57:32: 38000000
INFO @ Thu, 22 Dec 2016 03:57:34: 39000000
INFO @ Thu, 22 Dec 2016 03:57:36: 40000000
INFO @ Thu, 22 Dec 2016 03:57:37: 41000000
INFO @ Thu, 22 Dec 2016 03:57:39: 42000000
INFO @ Thu, 22 Dec 2016 03:57:41: 43000000
INFO @ Thu, 22 Dec 2016 03:57:42: 44000000
INFO @ Thu, 22 Dec 2016 03:57:44: 45000000
INFO @ Thu, 22 Dec 2016 03:57:46: 46000000
INFO @ Thu, 22 Dec 2016 03:57:47: 47000000
INFO @ Thu, 22 Dec 2016 03:57:49: 48000000
INFO @ Thu, 22 Dec 2016 03:57:51: 49000000
INFO @ Thu, 22 Dec 2016 03:57:52: 50000000
INFO @ Thu, 22 Dec 2016 03:57:54: #1 tag size is determined as 68 bps
INFO @ Thu, 22 Dec 2016 03:57:54: #1 tag size = 68
INFO @ Thu, 22 Dec 2016 03:57:54: #1 total tags in treatment: 6569602
INFO @ Thu, 22 Dec 2016 03:57:54: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:57:54: #1 finished!
INFO @ Thu, 22 Dec 2016 03:57:54: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:57:54: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:57:54: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 03:57:54: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:57:54: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 03:57:54: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:01:25: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 04:01:25: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 04:01:25: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 04:01:25: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 04:01:25: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:06:46: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:06:48: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 04:06:49: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 04:06:50: Done!
INFO @ Thu, 22 Dec 2016 04:06:54:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_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/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/align/pseudo_reps/rep1/pr2/SRR1370911_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 for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Thu, 22 Dec 2016 04:06:54: #1 read tag files...
INFO @ Thu, 22 Dec 2016 04:06:54: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 04:06:56: 1000000
INFO @ Thu, 22 Dec 2016 04:06:58: 2000000
INFO @ Thu, 22 Dec 2016 04:06:59: 3000000
INFO @ Thu, 22 Dec 2016 04:07:01: 4000000
INFO @ Thu, 22 Dec 2016 04:07:03: 5000000
INFO @ Thu, 22 Dec 2016 04:07:05: 6000000
INFO @ Thu, 22 Dec 2016 04:07:06: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 04:07:08: 1000000
INFO @ Thu, 22 Dec 2016 04:07:10: 2000000
INFO @ Thu, 22 Dec 2016 04:07:11: 3000000
INFO @ Thu, 22 Dec 2016 04:07:13: 4000000
INFO @ Thu, 22 Dec 2016 04:07:15: 5000000
INFO @ Thu, 22 Dec 2016 04:07:17: 6000000
INFO @ Thu, 22 Dec 2016 04:07:18: 7000000
INFO @ Thu, 22 Dec 2016 04:07:20: 8000000
INFO @ Thu, 22 Dec 2016 04:07:22: 9000000
INFO @ Thu, 22 Dec 2016 04:07:24: 10000000
INFO @ Thu, 22 Dec 2016 04:07:26: 11000000
INFO @ Thu, 22 Dec 2016 04:07:28: 12000000
INFO @ Thu, 22 Dec 2016 04:07:30: 13000000
INFO @ Thu, 22 Dec 2016 04:07:31: 14000000
INFO @ Thu, 22 Dec 2016 04:07:33: 15000000
INFO @ Thu, 22 Dec 2016 04:07:35: 16000000
INFO @ Thu, 22 Dec 2016 04:07:36: 17000000
INFO @ Thu, 22 Dec 2016 04:07:38: 18000000
INFO @ Thu, 22 Dec 2016 04:07:40: 19000000
INFO @ Thu, 22 Dec 2016 04:07:42: 20000000
INFO @ Thu, 22 Dec 2016 04:07:43: 21000000
INFO @ Thu, 22 Dec 2016 04:07:45: 22000000
INFO @ Thu, 22 Dec 2016 04:07:47: 23000000
INFO @ Thu, 22 Dec 2016 04:07:49: 24000000
INFO @ Thu, 22 Dec 2016 04:07:50: 25000000
INFO @ Thu, 22 Dec 2016 04:07:52: 26000000
INFO @ Thu, 22 Dec 2016 04:07:54: 27000000
INFO @ Thu, 22 Dec 2016 04:07:56: 28000000
INFO @ Thu, 22 Dec 2016 04:07:57: 29000000
INFO @ Thu, 22 Dec 2016 04:07:59: 30000000
INFO @ Thu, 22 Dec 2016 04:08:01: 31000000
INFO @ Thu, 22 Dec 2016 04:08:03: 32000000
INFO @ Thu, 22 Dec 2016 04:08:04: 33000000
INFO @ Thu, 22 Dec 2016 04:08:06: 34000000
INFO @ Thu, 22 Dec 2016 04:08:08: 35000000
INFO @ Thu, 22 Dec 2016 04:08:09: 36000000
INFO @ Thu, 22 Dec 2016 04:08:11: 37000000
INFO @ Thu, 22 Dec 2016 04:08:13: 38000000
INFO @ Thu, 22 Dec 2016 04:08:15: 39000000
INFO @ Thu, 22 Dec 2016 04:08:17: 40000000
INFO @ Thu, 22 Dec 2016 04:08:18: 41000000
INFO @ Thu, 22 Dec 2016 04:08:20: 42000000
INFO @ Thu, 22 Dec 2016 04:08:22: 43000000
INFO @ Thu, 22 Dec 2016 04:08:23: 44000000
INFO @ Thu, 22 Dec 2016 04:08:25: 45000000
INFO @ Thu, 22 Dec 2016 04:08:27: 46000000
INFO @ Thu, 22 Dec 2016 04:08:29: 47000000
INFO @ Thu, 22 Dec 2016 04:08:30: 48000000
INFO @ Thu, 22 Dec 2016 04:08:32: 49000000
INFO @ Thu, 22 Dec 2016 04:08:34: 50000000
INFO @ Thu, 22 Dec 2016 04:08:36: #1 tag size is determined as 68 bps
INFO @ Thu, 22 Dec 2016 04:08:36: #1 tag size = 68
INFO @ Thu, 22 Dec 2016 04:08:36: #1 total tags in treatment: 6569602
INFO @ Thu, 22 Dec 2016 04:08:36: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 04:08:36: #1 finished!
INFO @ Thu, 22 Dec 2016 04:08:36: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 04:08:36: #2 Skipped...
INFO @ Thu, 22 Dec 2016 04:08:36: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 04:08:36: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 04:08:36: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 04:08:36: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:16:11: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:24:12: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:24:19: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 04:24:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF621/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370911_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 04:24:30: Done!
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