| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 19504 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-12-21 14:15:07 | | End | 2016-12-21 14:15:07 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/signal/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/signal/macs2/rep1/SRR1370892_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/ZNF71/out/align/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/align/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1 -o "SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/signal/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/align/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1 -o "SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/signal/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_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--------------------
14939 (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 04:25:16:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/rep1/SRR1370892_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 04:25:16: #1 read tag files...
INFO @ Thu, 22 Dec 2016 04:25:16: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 04:25:18: 1000000
INFO @ Thu, 22 Dec 2016 04:25:20: 2000000
INFO @ Thu, 22 Dec 2016 04:25:21: 3000000
INFO @ Thu, 22 Dec 2016 04:25:23: 4000000
INFO @ Thu, 22 Dec 2016 04:25:24: 5000000
INFO @ Thu, 22 Dec 2016 04:25:26: 6000000
INFO @ Thu, 22 Dec 2016 04:25:28: 7000000
INFO @ Thu, 22 Dec 2016 04:25:29: 8000000
INFO @ Thu, 22 Dec 2016 04:25:31: 9000000
INFO @ Thu, 22 Dec 2016 04:25:32: 10000000
INFO @ Thu, 22 Dec 2016 04:25:34: 11000000
INFO @ Thu, 22 Dec 2016 04:25:36: 12000000
INFO @ Thu, 22 Dec 2016 04:25:37: 13000000
INFO @ Thu, 22 Dec 2016 04:25:39: 14000000
INFO @ Thu, 22 Dec 2016 04:25:40: 15000000
INFO @ Thu, 22 Dec 2016 04:25:42: 16000000
INFO @ Thu, 22 Dec 2016 04:25:43: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 04:25:45: 1000000
INFO @ Thu, 22 Dec 2016 04:25:47: 2000000
INFO @ Thu, 22 Dec 2016 04:25:48: 3000000
INFO @ Thu, 22 Dec 2016 04:25:50: 4000000
INFO @ Thu, 22 Dec 2016 04:25:52: 5000000
INFO @ Thu, 22 Dec 2016 04:25:53: 6000000
INFO @ Thu, 22 Dec 2016 04:25:55: 7000000
INFO @ Thu, 22 Dec 2016 04:25:57: 8000000
INFO @ Thu, 22 Dec 2016 04:25:58: 9000000
INFO @ Thu, 22 Dec 2016 04:26:00: 10000000
INFO @ Thu, 22 Dec 2016 04:26:01: 11000000
INFO @ Thu, 22 Dec 2016 04:26:03: 12000000
INFO @ Thu, 22 Dec 2016 04:26:05: 13000000
INFO @ Thu, 22 Dec 2016 04:26:06: 14000000
INFO @ Thu, 22 Dec 2016 04:26:08: 15000000
INFO @ Thu, 22 Dec 2016 04:26:10: 16000000
INFO @ Thu, 22 Dec 2016 04:26:11: 17000000
INFO @ Thu, 22 Dec 2016 04:26:13: 18000000
INFO @ Thu, 22 Dec 2016 04:26:15: 19000000
INFO @ Thu, 22 Dec 2016 04:26:16: 20000000
INFO @ Thu, 22 Dec 2016 04:26:18: 21000000
INFO @ Thu, 22 Dec 2016 04:26:19: 22000000
INFO @ Thu, 22 Dec 2016 04:26:21: 23000000
INFO @ Thu, 22 Dec 2016 04:26:22: 24000000
INFO @ Thu, 22 Dec 2016 04:26:24: 25000000
INFO @ Thu, 22 Dec 2016 04:26:26: 26000000
INFO @ Thu, 22 Dec 2016 04:26:27: 27000000
INFO @ Thu, 22 Dec 2016 04:26:29: 28000000
INFO @ Thu, 22 Dec 2016 04:26:31: 29000000
INFO @ Thu, 22 Dec 2016 04:26:32: 30000000
INFO @ Thu, 22 Dec 2016 04:26:34: 31000000
INFO @ Thu, 22 Dec 2016 04:26:36: 32000000
INFO @ Thu, 22 Dec 2016 04:26:37: 33000000
INFO @ Thu, 22 Dec 2016 04:26:39: 34000000
INFO @ Thu, 22 Dec 2016 04:26:40: 35000000
INFO @ Thu, 22 Dec 2016 04:26:42: 36000000
INFO @ Thu, 22 Dec 2016 04:26:44: 37000000
INFO @ Thu, 22 Dec 2016 04:26:45: 38000000
INFO @ Thu, 22 Dec 2016 04:26:47: 39000000
INFO @ Thu, 22 Dec 2016 04:26:49: 40000000
INFO @ Thu, 22 Dec 2016 04:26:50: 41000000
INFO @ Thu, 22 Dec 2016 04:26:52: 42000000
INFO @ Thu, 22 Dec 2016 04:26:53: 43000000
INFO @ Thu, 22 Dec 2016 04:26:55: 44000000
INFO @ Thu, 22 Dec 2016 04:26:57: 45000000
INFO @ Thu, 22 Dec 2016 04:26:58: 46000000
INFO @ Thu, 22 Dec 2016 04:27:00: 47000000
INFO @ Thu, 22 Dec 2016 04:27:02: 48000000
INFO @ Thu, 22 Dec 2016 04:27:03: 49000000
INFO @ Thu, 22 Dec 2016 04:27:05: 50000000
INFO @ Thu, 22 Dec 2016 04:27:07: #1 tag size is determined as 68 bps
INFO @ Thu, 22 Dec 2016 04:27:07: #1 tag size = 68
INFO @ Thu, 22 Dec 2016 04:27:07: #1 total tags in treatment: 16871958
INFO @ Thu, 22 Dec 2016 04:27:07: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 04:27:07: #1 finished!
INFO @ Thu, 22 Dec 2016 04:27:07: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 04:27:07: #2 Skipped...
INFO @ Thu, 22 Dec 2016 04:27:07: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 04:27:07: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 04:27:07: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 04:27:07: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:32:15: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 04:32:15: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 04:32:15: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 04:32:15: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 04:32:15: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:39:41: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:39:42: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 04:39:43: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 04:39:43: Done!
INFO @ Thu, 22 Dec 2016 04:39:47:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_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/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/rep1/SRR1370892_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 04:39:47: #1 read tag files...
INFO @ Thu, 22 Dec 2016 04:39:47: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 04:39:48: 1000000
INFO @ Thu, 22 Dec 2016 04:39:50: 2000000
INFO @ Thu, 22 Dec 2016 04:39:51: 3000000
INFO @ Thu, 22 Dec 2016 04:39:53: 4000000
INFO @ Thu, 22 Dec 2016 04:39:55: 5000000
INFO @ Thu, 22 Dec 2016 04:39:56: 6000000
INFO @ Thu, 22 Dec 2016 04:39:58: 7000000
INFO @ Thu, 22 Dec 2016 04:39:59: 8000000
INFO @ Thu, 22 Dec 2016 04:40:01: 9000000
INFO @ Thu, 22 Dec 2016 04:40:02: 10000000
INFO @ Thu, 22 Dec 2016 04:40:04: 11000000
INFO @ Thu, 22 Dec 2016 04:40:06: 12000000
INFO @ Thu, 22 Dec 2016 04:40:07: 13000000
INFO @ Thu, 22 Dec 2016 04:40:09: 14000000
INFO @ Thu, 22 Dec 2016 04:40:10: 15000000
INFO @ Thu, 22 Dec 2016 04:40:12: 16000000
INFO @ Thu, 22 Dec 2016 04:40:13: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 04:40:15: 1000000
INFO @ Thu, 22 Dec 2016 04:40:16: 2000000
INFO @ Thu, 22 Dec 2016 04:40:18: 3000000
INFO @ Thu, 22 Dec 2016 04:40:20: 4000000
INFO @ Thu, 22 Dec 2016 04:40:21: 5000000
INFO @ Thu, 22 Dec 2016 04:40:23: 6000000
INFO @ Thu, 22 Dec 2016 04:40:24: 7000000
INFO @ Thu, 22 Dec 2016 04:40:26: 8000000
INFO @ Thu, 22 Dec 2016 04:40:28: 9000000
INFO @ Thu, 22 Dec 2016 04:40:29: 10000000
INFO @ Thu, 22 Dec 2016 04:40:31: 11000000
INFO @ Thu, 22 Dec 2016 04:40:32: 12000000
INFO @ Thu, 22 Dec 2016 04:40:34: 13000000
INFO @ Thu, 22 Dec 2016 04:40:36: 14000000
INFO @ Thu, 22 Dec 2016 04:40:37: 15000000
INFO @ Thu, 22 Dec 2016 04:40:39: 16000000
INFO @ Thu, 22 Dec 2016 04:40:40: 17000000
INFO @ Thu, 22 Dec 2016 04:40:42: 18000000
INFO @ Thu, 22 Dec 2016 04:40:44: 19000000
INFO @ Thu, 22 Dec 2016 04:40:45: 20000000
INFO @ Thu, 22 Dec 2016 04:40:47: 21000000
INFO @ Thu, 22 Dec 2016 04:40:48: 22000000
INFO @ Thu, 22 Dec 2016 04:40:50: 23000000
INFO @ Thu, 22 Dec 2016 04:40:51: 24000000
INFO @ Thu, 22 Dec 2016 04:40:53: 25000000
INFO @ Thu, 22 Dec 2016 04:40:55: 26000000
INFO @ Thu, 22 Dec 2016 04:40:56: 27000000
INFO @ Thu, 22 Dec 2016 04:40:58: 28000000
INFO @ Thu, 22 Dec 2016 04:40:59: 29000000
INFO @ Thu, 22 Dec 2016 04:41:01: 30000000
INFO @ Thu, 22 Dec 2016 04:41:02: 31000000
INFO @ Thu, 22 Dec 2016 04:41:04: 32000000
INFO @ Thu, 22 Dec 2016 04:41:06: 33000000
INFO @ Thu, 22 Dec 2016 04:41:07: 34000000
INFO @ Thu, 22 Dec 2016 04:41:09: 35000000
INFO @ Thu, 22 Dec 2016 04:41:10: 36000000
INFO @ Thu, 22 Dec 2016 04:41:12: 37000000
INFO @ Thu, 22 Dec 2016 04:41:13: 38000000
INFO @ Thu, 22 Dec 2016 04:41:15: 39000000
INFO @ Thu, 22 Dec 2016 04:41:17: 40000000
INFO @ Thu, 22 Dec 2016 04:41:18: 41000000
INFO @ Thu, 22 Dec 2016 04:41:20: 42000000
INFO @ Thu, 22 Dec 2016 04:41:21: 43000000
INFO @ Thu, 22 Dec 2016 04:41:23: 44000000
INFO @ Thu, 22 Dec 2016 04:41:24: 45000000
INFO @ Thu, 22 Dec 2016 04:41:26: 46000000
INFO @ Thu, 22 Dec 2016 04:41:28: 47000000
INFO @ Thu, 22 Dec 2016 04:41:29: 48000000
INFO @ Thu, 22 Dec 2016 04:41:31: 49000000
INFO @ Thu, 22 Dec 2016 04:41:32: 50000000
INFO @ Thu, 22 Dec 2016 04:41:34: #1 tag size is determined as 68 bps
INFO @ Thu, 22 Dec 2016 04:41:34: #1 tag size = 68
INFO @ Thu, 22 Dec 2016 04:41:34: #1 total tags in treatment: 16871958
INFO @ Thu, 22 Dec 2016 04:41:34: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 04:41:34: #1 finished!
INFO @ Thu, 22 Dec 2016 04:41:34: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 04:41:34: #2 Skipped...
INFO @ Thu, 22 Dec 2016 04:41:34: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 04:41:34: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 04:41:34: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 04:41:34: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:45:09: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:48:39: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:48:44: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 04:48:49: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 04:48:52: Done!
INFO @ Thu, 22 Dec 2016 04:49:08: Read and build treatment bedGraph...
INFO @ Thu, 22 Dec 2016 04:49:45: Read and build control bedGraph...
INFO @ Thu, 22 Dec 2016 04:51:42: Build scoreTrackII...
INFO @ Thu, 22 Dec 2016 04:53:19: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 22 Dec 2016 04:59:04: Write bedGraph of scores...
INFO @ Thu, 22 Dec 2016 05:02:20: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/rep1/SRR1370892_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'!
Chromosome GL383567.1 isn't in /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes line 1 of stdin
--------------------Post mortem info--------------------
==============================================================
job_number: 19504
submission_time: Wed Dec 21 14:15:07 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/ZNF71
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/chipseq.bds.20161221_141500_509/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/ZNF71/chipseq.bds.20161221_141500_509/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=52466.ZNF71.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/ZNF71,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 | 19506 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:15:09 | | End | 2016-12-22 05:11:20 | | Elapsed | 14:56:10 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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--------------------
15516 (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 04:40:15:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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 04:40:15: #1 read tag files...
INFO @ Thu, 22 Dec 2016 04:40:15: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 04:40:17: 1000000
INFO @ Thu, 22 Dec 2016 04:40:19: 2000000
INFO @ Thu, 22 Dec 2016 04:40:21: 3000000
INFO @ Thu, 22 Dec 2016 04:40:22: 4000000
INFO @ Thu, 22 Dec 2016 04:40:24: 5000000
INFO @ Thu, 22 Dec 2016 04:40:26: 6000000
INFO @ Thu, 22 Dec 2016 04:40:28: 7000000
INFO @ Thu, 22 Dec 2016 04:40:29: 8000000
INFO @ Thu, 22 Dec 2016 04:40:31: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 04:40:32: 1000000
INFO @ Thu, 22 Dec 2016 04:40:34: 2000000
INFO @ Thu, 22 Dec 2016 04:40:36: 3000000
INFO @ Thu, 22 Dec 2016 04:40:38: 4000000
INFO @ Thu, 22 Dec 2016 04:40:39: 5000000
INFO @ Thu, 22 Dec 2016 04:40:41: 6000000
INFO @ Thu, 22 Dec 2016 04:40:43: 7000000
INFO @ Thu, 22 Dec 2016 04:40:44: 8000000
INFO @ Thu, 22 Dec 2016 04:40:46: 9000000
INFO @ Thu, 22 Dec 2016 04:40:48: 10000000
INFO @ Thu, 22 Dec 2016 04:40:49: 11000000
INFO @ Thu, 22 Dec 2016 04:40:51: 12000000
INFO @ Thu, 22 Dec 2016 04:40:53: 13000000
INFO @ Thu, 22 Dec 2016 04:40:54: 14000000
INFO @ Thu, 22 Dec 2016 04:40:56: 15000000
INFO @ Thu, 22 Dec 2016 04:40:58: 16000000
INFO @ Thu, 22 Dec 2016 04:41:00: 17000000
INFO @ Thu, 22 Dec 2016 04:41:02: 18000000
INFO @ Thu, 22 Dec 2016 04:41:03: 19000000
INFO @ Thu, 22 Dec 2016 04:41:05: 20000000
INFO @ Thu, 22 Dec 2016 04:41:07: 21000000
INFO @ Thu, 22 Dec 2016 04:41:09: 22000000
INFO @ Thu, 22 Dec 2016 04:41:10: 23000000
INFO @ Thu, 22 Dec 2016 04:41:12: 24000000
INFO @ Thu, 22 Dec 2016 04:41:14: 25000000
INFO @ Thu, 22 Dec 2016 04:41:16: 26000000
INFO @ Thu, 22 Dec 2016 04:41:17: 27000000
INFO @ Thu, 22 Dec 2016 04:41:19: 28000000
INFO @ Thu, 22 Dec 2016 04:41:21: 29000000
INFO @ Thu, 22 Dec 2016 04:41:22: 30000000
INFO @ Thu, 22 Dec 2016 04:41:24: 31000000
INFO @ Thu, 22 Dec 2016 04:41:26: 32000000
INFO @ Thu, 22 Dec 2016 04:41:28: 33000000
INFO @ Thu, 22 Dec 2016 04:41:29: 34000000
INFO @ Thu, 22 Dec 2016 04:41:31: 35000000
INFO @ Thu, 22 Dec 2016 04:41:33: 36000000
INFO @ Thu, 22 Dec 2016 04:41:34: 37000000
INFO @ Thu, 22 Dec 2016 04:41:36: 38000000
INFO @ Thu, 22 Dec 2016 04:41:38: 39000000
INFO @ Thu, 22 Dec 2016 04:41:39: 40000000
INFO @ Thu, 22 Dec 2016 04:41:41: 41000000
INFO @ Thu, 22 Dec 2016 04:41:43: 42000000
INFO @ Thu, 22 Dec 2016 04:41:44: 43000000
INFO @ Thu, 22 Dec 2016 04:41:46: 44000000
INFO @ Thu, 22 Dec 2016 04:41:48: 45000000
INFO @ Thu, 22 Dec 2016 04:41:49: 46000000
INFO @ Thu, 22 Dec 2016 04:41:51: 47000000
INFO @ Thu, 22 Dec 2016 04:41:53: 48000000
INFO @ Thu, 22 Dec 2016 04:41:54: 49000000
INFO @ Thu, 22 Dec 2016 04:41:56: 50000000
INFO @ Thu, 22 Dec 2016 04:41:58: #1 tag size is determined as 69 bps
INFO @ Thu, 22 Dec 2016 04:41:58: #1 tag size = 69
INFO @ Thu, 22 Dec 2016 04:41:58: #1 total tags in treatment: 8435979
INFO @ Thu, 22 Dec 2016 04:41:58: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 04:41:58: #1 finished!
INFO @ Thu, 22 Dec 2016 04:41:58: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 04:41:58: #2 Skipped...
INFO @ Thu, 22 Dec 2016 04:41:58: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 04:41:58: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 04:41:58: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 04:41:58: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:46:58: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 04:46:58: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 04:46:58: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 04:46:58: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 04:46:58: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:53:09: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:53:10: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 04:53:10: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 04:53:11: Done!
INFO @ Thu, 22 Dec 2016 04:53:15:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr1/SRR1370892_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 04:53:15: #1 read tag files...
INFO @ Thu, 22 Dec 2016 04:53:15: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 04:53:17: 1000000
INFO @ Thu, 22 Dec 2016 04:53:18: 2000000
INFO @ Thu, 22 Dec 2016 04:53:20: 3000000
INFO @ Thu, 22 Dec 2016 04:53:22: 4000000
INFO @ Thu, 22 Dec 2016 04:53:23: 5000000
INFO @ Thu, 22 Dec 2016 04:53:25: 6000000
INFO @ Thu, 22 Dec 2016 04:53:27: 7000000
INFO @ Thu, 22 Dec 2016 04:53:28: 8000000
INFO @ Thu, 22 Dec 2016 04:53:30: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 04:53:31: 1000000
INFO @ Thu, 22 Dec 2016 04:53:33: 2000000
INFO @ Thu, 22 Dec 2016 04:53:34: 3000000
INFO @ Thu, 22 Dec 2016 04:53:36: 4000000
INFO @ Thu, 22 Dec 2016 04:53:38: 5000000
INFO @ Thu, 22 Dec 2016 04:53:39: 6000000
INFO @ Thu, 22 Dec 2016 04:53:41: 7000000
INFO @ Thu, 22 Dec 2016 04:53:42: 8000000
INFO @ Thu, 22 Dec 2016 04:53:44: 9000000
INFO @ Thu, 22 Dec 2016 04:53:46: 10000000
INFO @ Thu, 22 Dec 2016 04:53:47: 11000000
INFO @ Thu, 22 Dec 2016 04:53:49: 12000000
INFO @ Thu, 22 Dec 2016 04:53:50: 13000000
INFO @ Thu, 22 Dec 2016 04:53:52: 14000000
INFO @ Thu, 22 Dec 2016 04:53:54: 15000000
INFO @ Thu, 22 Dec 2016 04:53:55: 16000000
INFO @ Thu, 22 Dec 2016 04:53:57: 17000000
INFO @ Thu, 22 Dec 2016 04:53:59: 18000000
INFO @ Thu, 22 Dec 2016 04:54:00: 19000000
INFO @ Thu, 22 Dec 2016 04:54:02: 20000000
INFO @ Thu, 22 Dec 2016 04:54:04: 21000000
INFO @ Thu, 22 Dec 2016 04:54:05: 22000000
INFO @ Thu, 22 Dec 2016 04:54:07: 23000000
INFO @ Thu, 22 Dec 2016 04:54:09: 24000000
INFO @ Thu, 22 Dec 2016 04:54:11: 25000000
INFO @ Thu, 22 Dec 2016 04:54:12: 26000000
INFO @ Thu, 22 Dec 2016 04:54:14: 27000000
INFO @ Thu, 22 Dec 2016 04:54:15: 28000000
INFO @ Thu, 22 Dec 2016 04:54:17: 29000000
INFO @ Thu, 22 Dec 2016 04:54:18: 30000000
INFO @ Thu, 22 Dec 2016 04:54:20: 31000000
INFO @ Thu, 22 Dec 2016 04:54:22: 32000000
INFO @ Thu, 22 Dec 2016 04:54:23: 33000000
INFO @ Thu, 22 Dec 2016 04:54:25: 34000000
INFO @ Thu, 22 Dec 2016 04:54:26: 35000000
INFO @ Thu, 22 Dec 2016 04:54:28: 36000000
INFO @ Thu, 22 Dec 2016 04:54:30: 37000000
INFO @ Thu, 22 Dec 2016 04:54:32: 38000000
INFO @ Thu, 22 Dec 2016 04:54:33: 39000000
INFO @ Thu, 22 Dec 2016 04:54:35: 40000000
INFO @ Thu, 22 Dec 2016 04:54:36: 41000000
INFO @ Thu, 22 Dec 2016 04:54:38: 42000000
INFO @ Thu, 22 Dec 2016 04:54:39: 43000000
INFO @ Thu, 22 Dec 2016 04:54:41: 44000000
INFO @ Thu, 22 Dec 2016 04:54:43: 45000000
INFO @ Thu, 22 Dec 2016 04:54:44: 46000000
INFO @ Thu, 22 Dec 2016 04:54:46: 47000000
INFO @ Thu, 22 Dec 2016 04:54:48: 48000000
INFO @ Thu, 22 Dec 2016 04:54:49: 49000000
INFO @ Thu, 22 Dec 2016 04:54:51: 50000000
INFO @ Thu, 22 Dec 2016 04:54:53: #1 tag size is determined as 69 bps
INFO @ Thu, 22 Dec 2016 04:54:53: #1 tag size = 69
INFO @ Thu, 22 Dec 2016 04:54:53: #1 total tags in treatment: 8435979
INFO @ Thu, 22 Dec 2016 04:54:53: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 04:54:53: #1 finished!
INFO @ Thu, 22 Dec 2016 04:54:53: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 04:54:53: #2 Skipped...
INFO @ Thu, 22 Dec 2016 04:54:53: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 04:54:53: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 04:54:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 04:54:53: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 05:02:32: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 05:10:38: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 05:10:45: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 05:10:50: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 05:10:54: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 19508 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:15:10 | | End | 2016-12-22 05:17:45 | | Elapsed | 15:02:34 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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--------------------
15654 (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 04:48:45:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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 04:48:45: #1 read tag files...
INFO @ Thu, 22 Dec 2016 04:48:45: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 04:48:47: 1000000
INFO @ Thu, 22 Dec 2016 04:48:49: 2000000
INFO @ Thu, 22 Dec 2016 04:48:51: 3000000
INFO @ Thu, 22 Dec 2016 04:48:52: 4000000
INFO @ Thu, 22 Dec 2016 04:48:54: 5000000
INFO @ Thu, 22 Dec 2016 04:48:56: 6000000
INFO @ Thu, 22 Dec 2016 04:48:57: 7000000
INFO @ Thu, 22 Dec 2016 04:48:59: 8000000
INFO @ Thu, 22 Dec 2016 04:49:01: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 04:49:02: 1000000
INFO @ Thu, 22 Dec 2016 04:49:04: 2000000
INFO @ Thu, 22 Dec 2016 04:49:06: 3000000
INFO @ Thu, 22 Dec 2016 04:49:08: 4000000
INFO @ Thu, 22 Dec 2016 04:49:09: 5000000
INFO @ Thu, 22 Dec 2016 04:49:11: 6000000
INFO @ Thu, 22 Dec 2016 04:49:12: 7000000
INFO @ Thu, 22 Dec 2016 04:49:14: 8000000
INFO @ Thu, 22 Dec 2016 04:49:15: 9000000
INFO @ Thu, 22 Dec 2016 04:49:17: 10000000
INFO @ Thu, 22 Dec 2016 04:49:19: 11000000
INFO @ Thu, 22 Dec 2016 04:49:20: 12000000
INFO @ Thu, 22 Dec 2016 04:49:22: 13000000
INFO @ Thu, 22 Dec 2016 04:49:24: 14000000
INFO @ Thu, 22 Dec 2016 04:49:25: 15000000
INFO @ Thu, 22 Dec 2016 04:49:27: 16000000
INFO @ Thu, 22 Dec 2016 04:49:29: 17000000
INFO @ Thu, 22 Dec 2016 04:49:30: 18000000
INFO @ Thu, 22 Dec 2016 04:49:32: 19000000
INFO @ Thu, 22 Dec 2016 04:49:33: 20000000
INFO @ Thu, 22 Dec 2016 04:49:35: 21000000
INFO @ Thu, 22 Dec 2016 04:49:36: 22000000
INFO @ Thu, 22 Dec 2016 04:49:38: 23000000
INFO @ Thu, 22 Dec 2016 04:49:40: 24000000
INFO @ Thu, 22 Dec 2016 04:49:41: 25000000
INFO @ Thu, 22 Dec 2016 04:49:43: 26000000
INFO @ Thu, 22 Dec 2016 04:49:44: 27000000
INFO @ Thu, 22 Dec 2016 04:49:46: 28000000
INFO @ Thu, 22 Dec 2016 04:49:48: 29000000
INFO @ Thu, 22 Dec 2016 04:49:49: 30000000
INFO @ Thu, 22 Dec 2016 04:49:51: 31000000
INFO @ Thu, 22 Dec 2016 04:49:53: 32000000
INFO @ Thu, 22 Dec 2016 04:49:54: 33000000
INFO @ Thu, 22 Dec 2016 04:49:56: 34000000
INFO @ Thu, 22 Dec 2016 04:49:57: 35000000
INFO @ Thu, 22 Dec 2016 04:49:59: 36000000
INFO @ Thu, 22 Dec 2016 04:50:00: 37000000
INFO @ Thu, 22 Dec 2016 04:50:02: 38000000
INFO @ Thu, 22 Dec 2016 04:50:04: 39000000
INFO @ Thu, 22 Dec 2016 04:50:06: 40000000
INFO @ Thu, 22 Dec 2016 04:50:08: 41000000
INFO @ Thu, 22 Dec 2016 04:50:10: 42000000
INFO @ Thu, 22 Dec 2016 04:50:11: 43000000
INFO @ Thu, 22 Dec 2016 04:50:13: 44000000
INFO @ Thu, 22 Dec 2016 04:50:14: 45000000
INFO @ Thu, 22 Dec 2016 04:50:16: 46000000
INFO @ Thu, 22 Dec 2016 04:50:17: 47000000
INFO @ Thu, 22 Dec 2016 04:50:19: 48000000
INFO @ Thu, 22 Dec 2016 04:50:21: 49000000
INFO @ Thu, 22 Dec 2016 04:50:22: 50000000
INFO @ Thu, 22 Dec 2016 04:50:24: #1 tag size is determined as 68 bps
INFO @ Thu, 22 Dec 2016 04:50:24: #1 tag size = 68
INFO @ Thu, 22 Dec 2016 04:50:24: #1 total tags in treatment: 8435979
INFO @ Thu, 22 Dec 2016 04:50:24: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 04:50:24: #1 finished!
INFO @ Thu, 22 Dec 2016 04:50:24: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 04:50:24: #2 Skipped...
INFO @ Thu, 22 Dec 2016 04:50:24: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 04:50:24: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 04:50:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 04:50:24: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:56:56: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 04:56:56: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 04:56:56: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 04:56:56: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 04:56:56: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 05:04:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 05:04:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 05:04:26: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 05:04:26: Done!
INFO @ Thu, 22 Dec 2016 05:04:32:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_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/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/align/pseudo_reps/rep1/pr2/SRR1370892_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 05:04:32: #1 read tag files...
INFO @ Thu, 22 Dec 2016 05:04:32: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 05:04:34: 1000000
INFO @ Thu, 22 Dec 2016 05:04:35: 2000000
INFO @ Thu, 22 Dec 2016 05:04:37: 3000000
INFO @ Thu, 22 Dec 2016 05:04:39: 4000000
INFO @ Thu, 22 Dec 2016 05:04:40: 5000000
INFO @ Thu, 22 Dec 2016 05:04:42: 6000000
INFO @ Thu, 22 Dec 2016 05:04:44: 7000000
INFO @ Thu, 22 Dec 2016 05:04:45: 8000000
INFO @ Thu, 22 Dec 2016 05:04:47: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 05:04:48: 1000000
INFO @ Thu, 22 Dec 2016 05:04:50: 2000000
INFO @ Thu, 22 Dec 2016 05:04:52: 3000000
INFO @ Thu, 22 Dec 2016 05:04:53: 4000000
INFO @ Thu, 22 Dec 2016 05:04:55: 5000000
INFO @ Thu, 22 Dec 2016 05:04:57: 6000000
INFO @ Thu, 22 Dec 2016 05:04:58: 7000000
INFO @ Thu, 22 Dec 2016 05:05:00: 8000000
INFO @ Thu, 22 Dec 2016 05:05:02: 9000000
INFO @ Thu, 22 Dec 2016 05:05:03: 10000000
INFO @ Thu, 22 Dec 2016 05:05:05: 11000000
INFO @ Thu, 22 Dec 2016 05:05:07: 12000000
INFO @ Thu, 22 Dec 2016 05:05:08: 13000000
INFO @ Thu, 22 Dec 2016 05:05:10: 14000000
INFO @ Thu, 22 Dec 2016 05:05:12: 15000000
INFO @ Thu, 22 Dec 2016 05:05:13: 16000000
INFO @ Thu, 22 Dec 2016 05:05:15: 17000000
INFO @ Thu, 22 Dec 2016 05:05:16: 18000000
INFO @ Thu, 22 Dec 2016 05:05:18: 19000000
INFO @ Thu, 22 Dec 2016 05:05:20: 20000000
INFO @ Thu, 22 Dec 2016 05:05:21: 21000000
INFO @ Thu, 22 Dec 2016 05:05:23: 22000000
INFO @ Thu, 22 Dec 2016 05:05:25: 23000000
INFO @ Thu, 22 Dec 2016 05:05:26: 24000000
INFO @ Thu, 22 Dec 2016 05:05:28: 25000000
INFO @ Thu, 22 Dec 2016 05:05:30: 26000000
INFO @ Thu, 22 Dec 2016 05:05:32: 27000000
INFO @ Thu, 22 Dec 2016 05:05:33: 28000000
INFO @ Thu, 22 Dec 2016 05:05:35: 29000000
INFO @ Thu, 22 Dec 2016 05:05:37: 30000000
INFO @ Thu, 22 Dec 2016 05:05:38: 31000000
INFO @ Thu, 22 Dec 2016 05:05:40: 32000000
INFO @ Thu, 22 Dec 2016 05:05:42: 33000000
INFO @ Thu, 22 Dec 2016 05:05:43: 34000000
INFO @ Thu, 22 Dec 2016 05:05:45: 35000000
INFO @ Thu, 22 Dec 2016 05:05:47: 36000000
INFO @ Thu, 22 Dec 2016 05:05:48: 37000000
INFO @ Thu, 22 Dec 2016 05:05:50: 38000000
INFO @ Thu, 22 Dec 2016 05:05:51: 39000000
INFO @ Thu, 22 Dec 2016 05:05:53: 40000000
INFO @ Thu, 22 Dec 2016 05:05:55: 41000000
INFO @ Thu, 22 Dec 2016 05:05:56: 42000000
INFO @ Thu, 22 Dec 2016 05:05:58: 43000000
INFO @ Thu, 22 Dec 2016 05:06:00: 44000000
INFO @ Thu, 22 Dec 2016 05:06:01: 45000000
INFO @ Thu, 22 Dec 2016 05:06:03: 46000000
INFO @ Thu, 22 Dec 2016 05:06:04: 47000000
INFO @ Thu, 22 Dec 2016 05:06:06: 48000000
INFO @ Thu, 22 Dec 2016 05:06:08: 49000000
INFO @ Thu, 22 Dec 2016 05:06:09: 50000000
INFO @ Thu, 22 Dec 2016 05:06:11: #1 tag size is determined as 68 bps
INFO @ Thu, 22 Dec 2016 05:06:11: #1 tag size = 68
INFO @ Thu, 22 Dec 2016 05:06:11: #1 total tags in treatment: 8435979
INFO @ Thu, 22 Dec 2016 05:06:11: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 05:06:11: #1 finished!
INFO @ Thu, 22 Dec 2016 05:06:11: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 05:06:11: #2 Skipped...
INFO @ Thu, 22 Dec 2016 05:06:11: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 05:06:11: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 05:06:11: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 05:06:11: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 05:13:04: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 05:17:12: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 05:17:18: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 05:17:23: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF71/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 05:17:27: Done!
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