| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 19474 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-12-21 14:13:57 | | End | 2016-12-21 14:13:57 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/signal/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/signal/macs2/rep1/SRR1370885_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/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 111
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1 -o "SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/signal/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/align/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1 -o "SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/signal/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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--------------------
7588 (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 @ Wed, 21 Dec 2016 21:06:44:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Wed, 21 Dec 2016 21:06:44: #1 read tag files...
INFO @ Wed, 21 Dec 2016 21:06:44: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 21:06:46: 1000000
INFO @ Wed, 21 Dec 2016 21:06:48: 2000000
INFO @ Wed, 21 Dec 2016 21:06:50: 3000000
INFO @ Wed, 21 Dec 2016 21:06:51: 4000000
INFO @ Wed, 21 Dec 2016 21:06:53: 5000000
INFO @ Wed, 21 Dec 2016 21:06:55: 6000000
INFO @ Wed, 21 Dec 2016 21:06:56: 7000000
INFO @ Wed, 21 Dec 2016 21:06:58: 8000000
INFO @ Wed, 21 Dec 2016 21:06:59: 9000000
INFO @ Wed, 21 Dec 2016 21:07:01: 10000000
INFO @ Wed, 21 Dec 2016 21:07:03: 11000000
INFO @ Wed, 21 Dec 2016 21:07:04: 12000000
INFO @ Wed, 21 Dec 2016 21:07:06: 13000000
INFO @ Wed, 21 Dec 2016 21:07:08: 14000000
INFO @ Wed, 21 Dec 2016 21:07:09: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 21:07:10: 1000000
INFO @ Wed, 21 Dec 2016 21:07:12: 2000000
INFO @ Wed, 21 Dec 2016 21:07:14: 3000000
INFO @ Wed, 21 Dec 2016 21:07:15: 4000000
INFO @ Wed, 21 Dec 2016 21:07:17: 5000000
INFO @ Wed, 21 Dec 2016 21:07:19: 6000000
INFO @ Wed, 21 Dec 2016 21:07:20: 7000000
INFO @ Wed, 21 Dec 2016 21:07:22: 8000000
INFO @ Wed, 21 Dec 2016 21:07:24: 9000000
INFO @ Wed, 21 Dec 2016 21:07:25: 10000000
INFO @ Wed, 21 Dec 2016 21:07:27: 11000000
INFO @ Wed, 21 Dec 2016 21:07:29: 12000000
INFO @ Wed, 21 Dec 2016 21:07:31: 13000000
INFO @ Wed, 21 Dec 2016 21:07:32: 14000000
INFO @ Wed, 21 Dec 2016 21:07:34: 15000000
INFO @ Wed, 21 Dec 2016 21:07:36: 16000000
INFO @ Wed, 21 Dec 2016 21:07:37: 17000000
INFO @ Wed, 21 Dec 2016 21:07:39: 18000000
INFO @ Wed, 21 Dec 2016 21:07:41: 19000000
INFO @ Wed, 21 Dec 2016 21:07:42: 20000000
INFO @ Wed, 21 Dec 2016 21:07:44: 21000000
INFO @ Wed, 21 Dec 2016 21:07:46: 22000000
INFO @ Wed, 21 Dec 2016 21:07:47: 23000000
INFO @ Wed, 21 Dec 2016 21:07:49: 24000000
INFO @ Wed, 21 Dec 2016 21:07:51: 25000000
INFO @ Wed, 21 Dec 2016 21:07:52: 26000000
INFO @ Wed, 21 Dec 2016 21:07:54: 27000000
INFO @ Wed, 21 Dec 2016 21:07:56: 28000000
INFO @ Wed, 21 Dec 2016 21:07:57: 29000000
INFO @ Wed, 21 Dec 2016 21:07:59: 30000000
INFO @ Wed, 21 Dec 2016 21:08:01: 31000000
INFO @ Wed, 21 Dec 2016 21:08:02: 32000000
INFO @ Wed, 21 Dec 2016 21:08:04: 33000000
INFO @ Wed, 21 Dec 2016 21:08:06: 34000000
INFO @ Wed, 21 Dec 2016 21:08:07: 35000000
INFO @ Wed, 21 Dec 2016 21:08:09: 36000000
INFO @ Wed, 21 Dec 2016 21:08:11: 37000000
INFO @ Wed, 21 Dec 2016 21:08:13: 38000000
INFO @ Wed, 21 Dec 2016 21:08:14: 39000000
INFO @ Wed, 21 Dec 2016 21:08:16: 40000000
INFO @ Wed, 21 Dec 2016 21:08:18: 41000000
INFO @ Wed, 21 Dec 2016 21:08:19: 42000000
INFO @ Wed, 21 Dec 2016 21:08:21: 43000000
INFO @ Wed, 21 Dec 2016 21:08:23: 44000000
INFO @ Wed, 21 Dec 2016 21:08:25: 45000000
INFO @ Wed, 21 Dec 2016 21:08:26: 46000000
INFO @ Wed, 21 Dec 2016 21:08:28: 47000000
INFO @ Wed, 21 Dec 2016 21:08:30: 48000000
INFO @ Wed, 21 Dec 2016 21:08:31: 49000000
INFO @ Wed, 21 Dec 2016 21:08:33: 50000000
INFO @ Wed, 21 Dec 2016 21:08:35: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 21:08:35: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 21:08:35: #1 total tags in treatment: 14380722
INFO @ Wed, 21 Dec 2016 21:08:35: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 21:08:35: #1 finished!
INFO @ Wed, 21 Dec 2016 21:08:35: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 21:08:35: #2 Skipped...
INFO @ Wed, 21 Dec 2016 21:08:35: #2 Use 150 as fragment length
INFO @ Wed, 21 Dec 2016 21:08:35: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 21:08:35: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Wed, 21 Dec 2016 21:08:35: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 21:12:19: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Wed, 21 Dec 2016 21:12:19: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Wed, 21 Dec 2016 21:12:19: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Wed, 21 Dec 2016 21:12:19: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Wed, 21 Dec 2016 21:12:19: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 21:17:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 21:17:38: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Wed, 21 Dec 2016 21:17:39: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Wed, 21 Dec 2016 21:17:40: Done!
INFO @ Wed, 21 Dec 2016 21:17:44:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff 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 @ Wed, 21 Dec 2016 21:17:44: #1 read tag files...
INFO @ Wed, 21 Dec 2016 21:17:44: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 21:17:46: 1000000
INFO @ Wed, 21 Dec 2016 21:17:48: 2000000
INFO @ Wed, 21 Dec 2016 21:17:50: 3000000
INFO @ Wed, 21 Dec 2016 21:17:51: 4000000
INFO @ Wed, 21 Dec 2016 21:17:53: 5000000
INFO @ Wed, 21 Dec 2016 21:17:55: 6000000
INFO @ Wed, 21 Dec 2016 21:17:56: 7000000
INFO @ Wed, 21 Dec 2016 21:17:58: 8000000
INFO @ Wed, 21 Dec 2016 21:18:00: 9000000
INFO @ Wed, 21 Dec 2016 21:18:02: 10000000
INFO @ Wed, 21 Dec 2016 21:18:03: 11000000
INFO @ Wed, 21 Dec 2016 21:18:05: 12000000
INFO @ Wed, 21 Dec 2016 21:18:07: 13000000
INFO @ Wed, 21 Dec 2016 21:18:08: 14000000
INFO @ Wed, 21 Dec 2016 21:18:09: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 21:18:11: 1000000
INFO @ Wed, 21 Dec 2016 21:18:13: 2000000
INFO @ Wed, 21 Dec 2016 21:18:15: 3000000
INFO @ Wed, 21 Dec 2016 21:18:17: 4000000
INFO @ Wed, 21 Dec 2016 21:18:18: 5000000
INFO @ Wed, 21 Dec 2016 21:18:20: 6000000
INFO @ Wed, 21 Dec 2016 21:18:22: 7000000
INFO @ Wed, 21 Dec 2016 21:18:24: 8000000
INFO @ Wed, 21 Dec 2016 21:18:25: 9000000
INFO @ Wed, 21 Dec 2016 21:18:27: 10000000
INFO @ Wed, 21 Dec 2016 21:18:29: 11000000
INFO @ Wed, 21 Dec 2016 21:18:31: 12000000
INFO @ Wed, 21 Dec 2016 21:18:32: 13000000
INFO @ Wed, 21 Dec 2016 21:18:34: 14000000
INFO @ Wed, 21 Dec 2016 21:18:36: 15000000
INFO @ Wed, 21 Dec 2016 21:18:37: 16000000
INFO @ Wed, 21 Dec 2016 21:18:39: 17000000
INFO @ Wed, 21 Dec 2016 21:18:41: 18000000
INFO @ Wed, 21 Dec 2016 21:18:43: 19000000
INFO @ Wed, 21 Dec 2016 21:18:44: 20000000
INFO @ Wed, 21 Dec 2016 21:18:46: 21000000
INFO @ Wed, 21 Dec 2016 21:18:48: 22000000
INFO @ Wed, 21 Dec 2016 21:18:50: 23000000
INFO @ Wed, 21 Dec 2016 21:18:51: 24000000
INFO @ Wed, 21 Dec 2016 21:18:53: 25000000
INFO @ Wed, 21 Dec 2016 21:18:55: 26000000
INFO @ Wed, 21 Dec 2016 21:18:57: 27000000
INFO @ Wed, 21 Dec 2016 21:18:58: 28000000
INFO @ Wed, 21 Dec 2016 21:19:00: 29000000
INFO @ Wed, 21 Dec 2016 21:19:02: 30000000
INFO @ Wed, 21 Dec 2016 21:19:04: 31000000
INFO @ Wed, 21 Dec 2016 21:19:05: 32000000
INFO @ Wed, 21 Dec 2016 21:19:07: 33000000
INFO @ Wed, 21 Dec 2016 21:19:09: 34000000
INFO @ Wed, 21 Dec 2016 21:19:10: 35000000
INFO @ Wed, 21 Dec 2016 21:19:12: 36000000
INFO @ Wed, 21 Dec 2016 21:19:14: 37000000
INFO @ Wed, 21 Dec 2016 21:19:16: 38000000
INFO @ Wed, 21 Dec 2016 21:19:17: 39000000
INFO @ Wed, 21 Dec 2016 21:19:19: 40000000
INFO @ Wed, 21 Dec 2016 21:19:21: 41000000
INFO @ Wed, 21 Dec 2016 21:19:23: 42000000
INFO @ Wed, 21 Dec 2016 21:19:24: 43000000
INFO @ Wed, 21 Dec 2016 21:19:26: 44000000
INFO @ Wed, 21 Dec 2016 21:19:28: 45000000
INFO @ Wed, 21 Dec 2016 21:19:30: 46000000
INFO @ Wed, 21 Dec 2016 21:19:31: 47000000
INFO @ Wed, 21 Dec 2016 21:19:33: 48000000
INFO @ Wed, 21 Dec 2016 21:19:35: 49000000
INFO @ Wed, 21 Dec 2016 21:19:36: 50000000
INFO @ Wed, 21 Dec 2016 21:19:38: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 21:19:38: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 21:19:38: #1 total tags in treatment: 14380722
INFO @ Wed, 21 Dec 2016 21:19:38: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 21:19:38: #1 finished!
INFO @ Wed, 21 Dec 2016 21:19:38: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 21:19:38: #2 Skipped...
INFO @ Wed, 21 Dec 2016 21:19:38: #2 Use 150 as fragment length
INFO @ Wed, 21 Dec 2016 21:19:38: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 21:19:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Wed, 21 Dec 2016 21:19:38: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 21:23:22: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 21:26:33: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 21:26:39: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Wed, 21 Dec 2016 21:26:42: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Wed, 21 Dec 2016 21:26:46: Done!
INFO @ Wed, 21 Dec 2016 21:27:02: Read and build treatment bedGraph...
INFO @ Wed, 21 Dec 2016 21:27:31: Read and build control bedGraph...
INFO @ Wed, 21 Dec 2016 21:29:19: Build scoreTrackII...
INFO @ Wed, 21 Dec 2016 21:30:08: Calculate scores comparing treatment and control by 'FE'...
INFO @ Wed, 21 Dec 2016 21:35:06: Write bedGraph of scores...
INFO @ Wed, 21 Dec 2016 21:37:44: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/rep1/SRR1370885_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: 19474
submission_time: Wed Dec 21 14:13:57 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/KLF14
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/chipseq.bds.20161221_141349_541/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/KLF14/chipseq.bds.20161221_141349_541/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=46361.KLF14.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/KLF14,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 | 19476 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:00 | | End | 2016-12-21 22:19:25 | | Elapsed | 08:05:25 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 111
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_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--------------------
8259 (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 @ Wed, 21 Dec 2016 21:58:14:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Wed, 21 Dec 2016 21:58:14: #1 read tag files...
INFO @ Wed, 21 Dec 2016 21:58:14: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 21:58:16: 1000000
INFO @ Wed, 21 Dec 2016 21:58:18: 2000000
INFO @ Wed, 21 Dec 2016 21:58:20: 3000000
INFO @ Wed, 21 Dec 2016 21:58:21: 4000000
INFO @ Wed, 21 Dec 2016 21:58:23: 5000000
INFO @ Wed, 21 Dec 2016 21:58:25: 6000000
INFO @ Wed, 21 Dec 2016 21:58:26: 7000000
INFO @ Wed, 21 Dec 2016 21:58:27: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 21:58:29: 1000000
INFO @ Wed, 21 Dec 2016 21:58:30: 2000000
INFO @ Wed, 21 Dec 2016 21:58:32: 3000000
INFO @ Wed, 21 Dec 2016 21:58:33: 4000000
INFO @ Wed, 21 Dec 2016 21:58:35: 5000000
INFO @ Wed, 21 Dec 2016 21:58:36: 6000000
INFO @ Wed, 21 Dec 2016 21:58:38: 7000000
INFO @ Wed, 21 Dec 2016 21:58:40: 8000000
INFO @ Wed, 21 Dec 2016 21:58:41: 9000000
INFO @ Wed, 21 Dec 2016 21:58:43: 10000000
INFO @ Wed, 21 Dec 2016 21:58:44: 11000000
INFO @ Wed, 21 Dec 2016 21:58:46: 12000000
INFO @ Wed, 21 Dec 2016 21:58:47: 13000000
INFO @ Wed, 21 Dec 2016 21:58:49: 14000000
INFO @ Wed, 21 Dec 2016 21:58:51: 15000000
INFO @ Wed, 21 Dec 2016 21:58:52: 16000000
INFO @ Wed, 21 Dec 2016 21:58:54: 17000000
INFO @ Wed, 21 Dec 2016 21:58:55: 18000000
INFO @ Wed, 21 Dec 2016 21:58:57: 19000000
INFO @ Wed, 21 Dec 2016 21:58:58: 20000000
INFO @ Wed, 21 Dec 2016 21:59:00: 21000000
INFO @ Wed, 21 Dec 2016 21:59:02: 22000000
INFO @ Wed, 21 Dec 2016 21:59:03: 23000000
INFO @ Wed, 21 Dec 2016 21:59:05: 24000000
INFO @ Wed, 21 Dec 2016 21:59:06: 25000000
INFO @ Wed, 21 Dec 2016 21:59:08: 26000000
INFO @ Wed, 21 Dec 2016 21:59:09: 27000000
INFO @ Wed, 21 Dec 2016 21:59:11: 28000000
INFO @ Wed, 21 Dec 2016 21:59:12: 29000000
INFO @ Wed, 21 Dec 2016 21:59:14: 30000000
INFO @ Wed, 21 Dec 2016 21:59:16: 31000000
INFO @ Wed, 21 Dec 2016 21:59:17: 32000000
INFO @ Wed, 21 Dec 2016 21:59:19: 33000000
INFO @ Wed, 21 Dec 2016 21:59:20: 34000000
INFO @ Wed, 21 Dec 2016 21:59:22: 35000000
INFO @ Wed, 21 Dec 2016 21:59:24: 36000000
INFO @ Wed, 21 Dec 2016 21:59:25: 37000000
INFO @ Wed, 21 Dec 2016 21:59:27: 38000000
INFO @ Wed, 21 Dec 2016 21:59:28: 39000000
INFO @ Wed, 21 Dec 2016 21:59:30: 40000000
INFO @ Wed, 21 Dec 2016 21:59:31: 41000000
INFO @ Wed, 21 Dec 2016 21:59:33: 42000000
INFO @ Wed, 21 Dec 2016 21:59:34: 43000000
INFO @ Wed, 21 Dec 2016 21:59:36: 44000000
INFO @ Wed, 21 Dec 2016 21:59:38: 45000000
INFO @ Wed, 21 Dec 2016 21:59:39: 46000000
INFO @ Wed, 21 Dec 2016 21:59:41: 47000000
INFO @ Wed, 21 Dec 2016 21:59:42: 48000000
INFO @ Wed, 21 Dec 2016 21:59:44: 49000000
INFO @ Wed, 21 Dec 2016 21:59:45: 50000000
INFO @ Wed, 21 Dec 2016 21:59:47: #1 tag size is determined as 67 bps
INFO @ Wed, 21 Dec 2016 21:59:47: #1 tag size = 67
INFO @ Wed, 21 Dec 2016 21:59:47: #1 total tags in treatment: 7190361
INFO @ Wed, 21 Dec 2016 21:59:47: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 21:59:47: #1 finished!
INFO @ Wed, 21 Dec 2016 21:59:47: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 21:59:47: #2 Skipped...
INFO @ Wed, 21 Dec 2016 21:59:47: #2 Use 150 as fragment length
INFO @ Wed, 21 Dec 2016 21:59:47: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 21:59:47: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Wed, 21 Dec 2016 21:59:47: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 22:03:25: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Wed, 21 Dec 2016 22:03:25: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Wed, 21 Dec 2016 22:03:25: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Wed, 21 Dec 2016 22:03:25: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Wed, 21 Dec 2016 22:03:25: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 22:08:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 22:08:38: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Wed, 21 Dec 2016 22:08:39: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Wed, 21 Dec 2016 22:08:40: Done!
INFO @ Wed, 21 Dec 2016 22:08:45:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff 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 @ Wed, 21 Dec 2016 22:08:45: #1 read tag files...
INFO @ Wed, 21 Dec 2016 22:08:45: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 22:08:47: 1000000
INFO @ Wed, 21 Dec 2016 22:08:49: 2000000
INFO @ Wed, 21 Dec 2016 22:08:51: 3000000
INFO @ Wed, 21 Dec 2016 22:08:52: 4000000
INFO @ Wed, 21 Dec 2016 22:08:54: 5000000
INFO @ Wed, 21 Dec 2016 22:08:56: 6000000
INFO @ Wed, 21 Dec 2016 22:08:58: 7000000
INFO @ Wed, 21 Dec 2016 22:08:59: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 22:09:00: 1000000
INFO @ Wed, 21 Dec 2016 22:09:02: 2000000
INFO @ Wed, 21 Dec 2016 22:09:04: 3000000
INFO @ Wed, 21 Dec 2016 22:09:06: 4000000
INFO @ Wed, 21 Dec 2016 22:09:08: 5000000
INFO @ Wed, 21 Dec 2016 22:09:09: 6000000
INFO @ Wed, 21 Dec 2016 22:09:11: 7000000
INFO @ Wed, 21 Dec 2016 22:09:13: 8000000
INFO @ Wed, 21 Dec 2016 22:09:15: 9000000
INFO @ Wed, 21 Dec 2016 22:09:17: 10000000
INFO @ Wed, 21 Dec 2016 22:09:19: 11000000
INFO @ Wed, 21 Dec 2016 22:09:20: 12000000
INFO @ Wed, 21 Dec 2016 22:09:22: 13000000
INFO @ Wed, 21 Dec 2016 22:09:24: 14000000
INFO @ Wed, 21 Dec 2016 22:09:26: 15000000
INFO @ Wed, 21 Dec 2016 22:09:27: 16000000
INFO @ Wed, 21 Dec 2016 22:09:29: 17000000
INFO @ Wed, 21 Dec 2016 22:09:31: 18000000
INFO @ Wed, 21 Dec 2016 22:09:33: 19000000
INFO @ Wed, 21 Dec 2016 22:09:34: 20000000
INFO @ Wed, 21 Dec 2016 22:09:36: 21000000
INFO @ Wed, 21 Dec 2016 22:09:38: 22000000
INFO @ Wed, 21 Dec 2016 22:09:40: 23000000
INFO @ Wed, 21 Dec 2016 22:09:41: 24000000
INFO @ Wed, 21 Dec 2016 22:09:43: 25000000
INFO @ Wed, 21 Dec 2016 22:09:45: 26000000
INFO @ Wed, 21 Dec 2016 22:09:47: 27000000
INFO @ Wed, 21 Dec 2016 22:09:48: 28000000
INFO @ Wed, 21 Dec 2016 22:09:50: 29000000
INFO @ Wed, 21 Dec 2016 22:09:52: 30000000
INFO @ Wed, 21 Dec 2016 22:09:54: 31000000
INFO @ Wed, 21 Dec 2016 22:09:56: 32000000
INFO @ Wed, 21 Dec 2016 22:09:57: 33000000
INFO @ Wed, 21 Dec 2016 22:09:59: 34000000
INFO @ Wed, 21 Dec 2016 22:10:01: 35000000
INFO @ Wed, 21 Dec 2016 22:10:03: 36000000
INFO @ Wed, 21 Dec 2016 22:10:04: 37000000
INFO @ Wed, 21 Dec 2016 22:10:06: 38000000
INFO @ Wed, 21 Dec 2016 22:10:08: 39000000
INFO @ Wed, 21 Dec 2016 22:10:10: 40000000
INFO @ Wed, 21 Dec 2016 22:10:11: 41000000
INFO @ Wed, 21 Dec 2016 22:10:13: 42000000
INFO @ Wed, 21 Dec 2016 22:10:15: 43000000
INFO @ Wed, 21 Dec 2016 22:10:17: 44000000
INFO @ Wed, 21 Dec 2016 22:10:19: 45000000
INFO @ Wed, 21 Dec 2016 22:10:21: 46000000
INFO @ Wed, 21 Dec 2016 22:10:23: 47000000
INFO @ Wed, 21 Dec 2016 22:10:24: 48000000
INFO @ Wed, 21 Dec 2016 22:10:26: 49000000
INFO @ Wed, 21 Dec 2016 22:10:28: 50000000
INFO @ Wed, 21 Dec 2016 22:10:30: #1 tag size is determined as 67 bps
INFO @ Wed, 21 Dec 2016 22:10:30: #1 tag size = 67
INFO @ Wed, 21 Dec 2016 22:10:30: #1 total tags in treatment: 7190361
INFO @ Wed, 21 Dec 2016 22:10:30: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 22:10:30: #1 finished!
INFO @ Wed, 21 Dec 2016 22:10:30: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 22:10:30: #2 Skipped...
INFO @ Wed, 21 Dec 2016 22:10:30: #2 Use 150 as fragment length
INFO @ Wed, 21 Dec 2016 22:10:30: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 22:10:30: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Wed, 21 Dec 2016 22:10:30: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 22:14:31: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 22:18:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 22:18:55: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Wed, 21 Dec 2016 22:19:00: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Wed, 21 Dec 2016 22:19:05: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 19477 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:00 | | End | 2016-12-21 22:40:42 | | Elapsed | 08:26:42 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 111
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_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--------------------
8523 (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 @ Wed, 21 Dec 2016 22:19:45:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Wed, 21 Dec 2016 22:19:45: #1 read tag files...
INFO @ Wed, 21 Dec 2016 22:19:45: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 22:19:47: 1000000
INFO @ Wed, 21 Dec 2016 22:19:49: 2000000
INFO @ Wed, 21 Dec 2016 22:19:50: 3000000
INFO @ Wed, 21 Dec 2016 22:19:52: 4000000
INFO @ Wed, 21 Dec 2016 22:19:54: 5000000
INFO @ Wed, 21 Dec 2016 22:19:55: 6000000
INFO @ Wed, 21 Dec 2016 22:19:57: 7000000
INFO @ Wed, 21 Dec 2016 22:19:58: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 22:19:59: 1000000
INFO @ Wed, 21 Dec 2016 22:20:01: 2000000
INFO @ Wed, 21 Dec 2016 22:20:03: 3000000
INFO @ Wed, 21 Dec 2016 22:20:04: 4000000
INFO @ Wed, 21 Dec 2016 22:20:06: 5000000
INFO @ Wed, 21 Dec 2016 22:20:07: 6000000
INFO @ Wed, 21 Dec 2016 22:20:09: 7000000
INFO @ Wed, 21 Dec 2016 22:20:10: 8000000
INFO @ Wed, 21 Dec 2016 22:20:12: 9000000
INFO @ Wed, 21 Dec 2016 22:20:13: 10000000
INFO @ Wed, 21 Dec 2016 22:20:15: 11000000
INFO @ Wed, 21 Dec 2016 22:20:16: 12000000
INFO @ Wed, 21 Dec 2016 22:20:18: 13000000
INFO @ Wed, 21 Dec 2016 22:20:20: 14000000
INFO @ Wed, 21 Dec 2016 22:20:21: 15000000
INFO @ Wed, 21 Dec 2016 22:20:23: 16000000
INFO @ Wed, 21 Dec 2016 22:20:24: 17000000
INFO @ Wed, 21 Dec 2016 22:20:26: 18000000
INFO @ Wed, 21 Dec 2016 22:20:27: 19000000
INFO @ Wed, 21 Dec 2016 22:20:29: 20000000
INFO @ Wed, 21 Dec 2016 22:20:31: 21000000
INFO @ Wed, 21 Dec 2016 22:20:32: 22000000
INFO @ Wed, 21 Dec 2016 22:20:34: 23000000
INFO @ Wed, 21 Dec 2016 22:20:35: 24000000
INFO @ Wed, 21 Dec 2016 22:20:37: 25000000
INFO @ Wed, 21 Dec 2016 22:20:38: 26000000
INFO @ Wed, 21 Dec 2016 22:20:40: 27000000
INFO @ Wed, 21 Dec 2016 22:20:41: 28000000
INFO @ Wed, 21 Dec 2016 22:20:43: 29000000
INFO @ Wed, 21 Dec 2016 22:20:44: 30000000
INFO @ Wed, 21 Dec 2016 22:20:46: 31000000
INFO @ Wed, 21 Dec 2016 22:20:47: 32000000
INFO @ Wed, 21 Dec 2016 22:20:49: 33000000
INFO @ Wed, 21 Dec 2016 22:20:51: 34000000
INFO @ Wed, 21 Dec 2016 22:20:52: 35000000
INFO @ Wed, 21 Dec 2016 22:20:54: 36000000
INFO @ Wed, 21 Dec 2016 22:20:55: 37000000
INFO @ Wed, 21 Dec 2016 22:20:57: 38000000
INFO @ Wed, 21 Dec 2016 22:20:58: 39000000
INFO @ Wed, 21 Dec 2016 22:21:00: 40000000
INFO @ Wed, 21 Dec 2016 22:21:01: 41000000
INFO @ Wed, 21 Dec 2016 22:21:03: 42000000
INFO @ Wed, 21 Dec 2016 22:21:04: 43000000
INFO @ Wed, 21 Dec 2016 22:21:06: 44000000
INFO @ Wed, 21 Dec 2016 22:21:07: 45000000
INFO @ Wed, 21 Dec 2016 22:21:09: 46000000
INFO @ Wed, 21 Dec 2016 22:21:11: 47000000
INFO @ Wed, 21 Dec 2016 22:21:12: 48000000
INFO @ Wed, 21 Dec 2016 22:21:14: 49000000
INFO @ Wed, 21 Dec 2016 22:21:15: 50000000
INFO @ Wed, 21 Dec 2016 22:21:17: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 22:21:17: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 22:21:17: #1 total tags in treatment: 7190361
INFO @ Wed, 21 Dec 2016 22:21:17: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 22:21:17: #1 finished!
INFO @ Wed, 21 Dec 2016 22:21:17: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 22:21:17: #2 Skipped...
INFO @ Wed, 21 Dec 2016 22:21:17: #2 Use 150 as fragment length
INFO @ Wed, 21 Dec 2016 22:21:17: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 22:21:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Wed, 21 Dec 2016 22:21:17: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 22:25:16: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Wed, 21 Dec 2016 22:25:16: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Wed, 21 Dec 2016 22:25:16: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Wed, 21 Dec 2016 22:25:16: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Wed, 21 Dec 2016 22:25:16: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 22:30:30: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 22:30:32: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Wed, 21 Dec 2016 22:30:34: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Wed, 21 Dec 2016 22:30:35: Done!
INFO @ Wed, 21 Dec 2016 22:30:39:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff 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 @ Wed, 21 Dec 2016 22:30:39: #1 read tag files...
INFO @ Wed, 21 Dec 2016 22:30:39: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 22:30:41: 1000000
INFO @ Wed, 21 Dec 2016 22:30:43: 2000000
INFO @ Wed, 21 Dec 2016 22:30:44: 3000000
INFO @ Wed, 21 Dec 2016 22:30:46: 4000000
INFO @ Wed, 21 Dec 2016 22:30:48: 5000000
INFO @ Wed, 21 Dec 2016 22:30:49: 6000000
INFO @ Wed, 21 Dec 2016 22:30:51: 7000000
INFO @ Wed, 21 Dec 2016 22:30:52: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 22:30:53: 1000000
INFO @ Wed, 21 Dec 2016 22:30:55: 2000000
INFO @ Wed, 21 Dec 2016 22:30:57: 3000000
INFO @ Wed, 21 Dec 2016 22:30:58: 4000000
INFO @ Wed, 21 Dec 2016 22:31:00: 5000000
INFO @ Wed, 21 Dec 2016 22:31:01: 6000000
INFO @ Wed, 21 Dec 2016 22:31:03: 7000000
INFO @ Wed, 21 Dec 2016 22:31:04: 8000000
INFO @ Wed, 21 Dec 2016 22:31:06: 9000000
INFO @ Wed, 21 Dec 2016 22:31:07: 10000000
INFO @ Wed, 21 Dec 2016 22:31:09: 11000000
INFO @ Wed, 21 Dec 2016 22:31:11: 12000000
INFO @ Wed, 21 Dec 2016 22:31:12: 13000000
INFO @ Wed, 21 Dec 2016 22:31:14: 14000000
INFO @ Wed, 21 Dec 2016 22:31:15: 15000000
INFO @ Wed, 21 Dec 2016 22:31:17: 16000000
INFO @ Wed, 21 Dec 2016 22:31:18: 17000000
INFO @ Wed, 21 Dec 2016 22:31:20: 18000000
INFO @ Wed, 21 Dec 2016 22:31:21: 19000000
INFO @ Wed, 21 Dec 2016 22:31:23: 20000000
INFO @ Wed, 21 Dec 2016 22:31:24: 21000000
INFO @ Wed, 21 Dec 2016 22:31:26: 22000000
INFO @ Wed, 21 Dec 2016 22:31:28: 23000000
INFO @ Wed, 21 Dec 2016 22:31:29: 24000000
INFO @ Wed, 21 Dec 2016 22:31:31: 25000000
INFO @ Wed, 21 Dec 2016 22:31:32: 26000000
INFO @ Wed, 21 Dec 2016 22:31:34: 27000000
INFO @ Wed, 21 Dec 2016 22:31:35: 28000000
INFO @ Wed, 21 Dec 2016 22:31:37: 29000000
INFO @ Wed, 21 Dec 2016 22:31:38: 30000000
INFO @ Wed, 21 Dec 2016 22:31:40: 31000000
INFO @ Wed, 21 Dec 2016 22:31:42: 32000000
INFO @ Wed, 21 Dec 2016 22:31:43: 33000000
INFO @ Wed, 21 Dec 2016 22:31:45: 34000000
INFO @ Wed, 21 Dec 2016 22:31:46: 35000000
INFO @ Wed, 21 Dec 2016 22:31:48: 36000000
INFO @ Wed, 21 Dec 2016 22:31:49: 37000000
INFO @ Wed, 21 Dec 2016 22:31:51: 38000000
INFO @ Wed, 21 Dec 2016 22:31:53: 39000000
INFO @ Wed, 21 Dec 2016 22:31:54: 40000000
INFO @ Wed, 21 Dec 2016 22:31:56: 41000000
INFO @ Wed, 21 Dec 2016 22:31:57: 42000000
INFO @ Wed, 21 Dec 2016 22:31:59: 43000000
INFO @ Wed, 21 Dec 2016 22:32:00: 44000000
INFO @ Wed, 21 Dec 2016 22:32:02: 45000000
INFO @ Wed, 21 Dec 2016 22:32:04: 46000000
INFO @ Wed, 21 Dec 2016 22:32:05: 47000000
INFO @ Wed, 21 Dec 2016 22:32:07: 48000000
INFO @ Wed, 21 Dec 2016 22:32:08: 49000000
INFO @ Wed, 21 Dec 2016 22:32:10: 50000000
INFO @ Wed, 21 Dec 2016 22:32:11: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 22:32:11: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 22:32:11: #1 total tags in treatment: 7190361
INFO @ Wed, 21 Dec 2016 22:32:11: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 22:32:11: #1 finished!
INFO @ Wed, 21 Dec 2016 22:32:11: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 22:32:11: #2 Skipped...
INFO @ Wed, 21 Dec 2016 22:32:11: #2 Use 150 as fragment length
INFO @ Wed, 21 Dec 2016 22:32:11: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 22:32:11: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Wed, 21 Dec 2016 22:32:11: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 22:36:13: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 22:40:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 22:40:13: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Wed, 21 Dec 2016 22:40:18: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Wed, 21 Dec 2016 22:40:23: Done!
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