| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 19491 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:53 | | End | 2016-12-21 14:14:53 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/signal/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/signal/macs2/rep1/SRR1370893_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/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1 -o "SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/signal/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1 -o "SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/signal/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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--------------------
12305 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Thu, 22 Dec 2016 02:36:14:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 22 Dec 2016 02:36:14: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:36:14: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:36:16: 1000000
INFO @ Thu, 22 Dec 2016 02:36:18: 2000000
INFO @ Thu, 22 Dec 2016 02:36:19: 3000000
INFO @ Thu, 22 Dec 2016 02:36:21: 4000000
INFO @ Thu, 22 Dec 2016 02:36:22: 5000000
INFO @ Thu, 22 Dec 2016 02:36:24: 6000000
INFO @ Thu, 22 Dec 2016 02:36:26: 7000000
INFO @ Thu, 22 Dec 2016 02:36:27: 8000000
INFO @ Thu, 22 Dec 2016 02:36:29: 9000000
INFO @ Thu, 22 Dec 2016 02:36:30: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:36:32: 1000000
INFO @ Thu, 22 Dec 2016 02:36:34: 2000000
INFO @ Thu, 22 Dec 2016 02:36:35: 3000000
INFO @ Thu, 22 Dec 2016 02:36:37: 4000000
INFO @ Thu, 22 Dec 2016 02:36:39: 5000000
INFO @ Thu, 22 Dec 2016 02:36:40: 6000000
INFO @ Thu, 22 Dec 2016 02:36:42: 7000000
INFO @ Thu, 22 Dec 2016 02:36:44: 8000000
INFO @ Thu, 22 Dec 2016 02:36:45: 9000000
INFO @ Thu, 22 Dec 2016 02:36:47: 10000000
INFO @ Thu, 22 Dec 2016 02:36:49: 11000000
INFO @ Thu, 22 Dec 2016 02:36:50: 12000000
INFO @ Thu, 22 Dec 2016 02:36:52: 13000000
INFO @ Thu, 22 Dec 2016 02:36:53: 14000000
INFO @ Thu, 22 Dec 2016 02:36:55: 15000000
INFO @ Thu, 22 Dec 2016 02:36:57: 16000000
INFO @ Thu, 22 Dec 2016 02:36:58: 17000000
INFO @ Thu, 22 Dec 2016 02:37:00: 18000000
INFO @ Thu, 22 Dec 2016 02:37:02: 19000000
INFO @ Thu, 22 Dec 2016 02:37:03: 20000000
INFO @ Thu, 22 Dec 2016 02:37:05: 21000000
INFO @ Thu, 22 Dec 2016 02:37:06: 22000000
INFO @ Thu, 22 Dec 2016 02:37:08: 23000000
INFO @ Thu, 22 Dec 2016 02:37:10: 24000000
INFO @ Thu, 22 Dec 2016 02:37:11: 25000000
INFO @ Thu, 22 Dec 2016 02:37:13: 26000000
INFO @ Thu, 22 Dec 2016 02:37:15: 27000000
INFO @ Thu, 22 Dec 2016 02:37:16: 28000000
INFO @ Thu, 22 Dec 2016 02:37:18: 29000000
INFO @ Thu, 22 Dec 2016 02:37:20: 30000000
INFO @ Thu, 22 Dec 2016 02:37:21: 31000000
INFO @ Thu, 22 Dec 2016 02:37:23: 32000000
INFO @ Thu, 22 Dec 2016 02:37:25: 33000000
INFO @ Thu, 22 Dec 2016 02:37:26: 34000000
INFO @ Thu, 22 Dec 2016 02:37:28: 35000000
INFO @ Thu, 22 Dec 2016 02:37:29: 36000000
INFO @ Thu, 22 Dec 2016 02:37:31: 37000000
INFO @ Thu, 22 Dec 2016 02:37:33: 38000000
INFO @ Thu, 22 Dec 2016 02:37:35: 39000000
INFO @ Thu, 22 Dec 2016 02:37:36: 40000000
INFO @ Thu, 22 Dec 2016 02:37:38: 41000000
INFO @ Thu, 22 Dec 2016 02:37:39: 42000000
INFO @ Thu, 22 Dec 2016 02:37:41: 43000000
INFO @ Thu, 22 Dec 2016 02:37:43: 44000000
INFO @ Thu, 22 Dec 2016 02:37:44: 45000000
INFO @ Thu, 22 Dec 2016 02:37:46: 46000000
INFO @ Thu, 22 Dec 2016 02:37:48: 47000000
INFO @ Thu, 22 Dec 2016 02:37:49: 48000000
INFO @ Thu, 22 Dec 2016 02:37:51: 49000000
INFO @ Thu, 22 Dec 2016 02:37:52: 50000000
INFO @ Thu, 22 Dec 2016 02:37:54: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 02:37:54: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 02:37:54: #1 total tags in treatment: 9914366
INFO @ Thu, 22 Dec 2016 02:37:54: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:37:54: #1 finished!
INFO @ Thu, 22 Dec 2016 02:37:54: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:37:54: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:37:54: #2 Use 135 as fragment length
INFO @ Thu, 22 Dec 2016 02:37:54: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:37:54: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 02:37:54: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:41:15: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 02:41:15: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 02:41:15: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 02:41:15: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 02:41:15: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 02:46:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 02:46:23: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 02:46:24: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 02:46:24: Done!
INFO @ Thu, 22 Dec 2016 02:46:28:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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 02:46:28: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:46:28: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:46:30: 1000000
INFO @ Thu, 22 Dec 2016 02:46:31: 2000000
INFO @ Thu, 22 Dec 2016 02:46:33: 3000000
INFO @ Thu, 22 Dec 2016 02:46:34: 4000000
INFO @ Thu, 22 Dec 2016 02:46:36: 5000000
INFO @ Thu, 22 Dec 2016 02:46:37: 6000000
INFO @ Thu, 22 Dec 2016 02:46:39: 7000000
INFO @ Thu, 22 Dec 2016 02:46:41: 8000000
INFO @ Thu, 22 Dec 2016 02:46:42: 9000000
INFO @ Thu, 22 Dec 2016 02:46:44: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:46:45: 1000000
INFO @ Thu, 22 Dec 2016 02:46:47: 2000000
INFO @ Thu, 22 Dec 2016 02:46:49: 3000000
INFO @ Thu, 22 Dec 2016 02:46:50: 4000000
INFO @ Thu, 22 Dec 2016 02:46:52: 5000000
INFO @ Thu, 22 Dec 2016 02:46:53: 6000000
INFO @ Thu, 22 Dec 2016 02:46:55: 7000000
INFO @ Thu, 22 Dec 2016 02:46:57: 8000000
INFO @ Thu, 22 Dec 2016 02:46:58: 9000000
INFO @ Thu, 22 Dec 2016 02:47:00: 10000000
INFO @ Thu, 22 Dec 2016 02:47:01: 11000000
INFO @ Thu, 22 Dec 2016 02:47:03: 12000000
INFO @ Thu, 22 Dec 2016 02:47:04: 13000000
INFO @ Thu, 22 Dec 2016 02:47:06: 14000000
INFO @ Thu, 22 Dec 2016 02:47:07: 15000000
INFO @ Thu, 22 Dec 2016 02:47:09: 16000000
INFO @ Thu, 22 Dec 2016 02:47:10: 17000000
INFO @ Thu, 22 Dec 2016 02:47:12: 18000000
INFO @ Thu, 22 Dec 2016 02:47:14: 19000000
INFO @ Thu, 22 Dec 2016 02:47:15: 20000000
INFO @ Thu, 22 Dec 2016 02:47:17: 21000000
INFO @ Thu, 22 Dec 2016 02:47:18: 22000000
INFO @ Thu, 22 Dec 2016 02:47:20: 23000000
INFO @ Thu, 22 Dec 2016 02:47:21: 24000000
INFO @ Thu, 22 Dec 2016 02:47:23: 25000000
INFO @ Thu, 22 Dec 2016 02:47:24: 26000000
INFO @ Thu, 22 Dec 2016 02:47:26: 27000000
INFO @ Thu, 22 Dec 2016 02:47:27: 28000000
INFO @ Thu, 22 Dec 2016 02:47:29: 29000000
INFO @ Thu, 22 Dec 2016 02:47:31: 30000000
INFO @ Thu, 22 Dec 2016 02:47:32: 31000000
INFO @ Thu, 22 Dec 2016 02:47:34: 32000000
INFO @ Thu, 22 Dec 2016 02:47:35: 33000000
INFO @ Thu, 22 Dec 2016 02:47:37: 34000000
INFO @ Thu, 22 Dec 2016 02:47:38: 35000000
INFO @ Thu, 22 Dec 2016 02:47:40: 36000000
INFO @ Thu, 22 Dec 2016 02:47:41: 37000000
INFO @ Thu, 22 Dec 2016 02:47:43: 38000000
INFO @ Thu, 22 Dec 2016 02:47:45: 39000000
INFO @ Thu, 22 Dec 2016 02:47:46: 40000000
INFO @ Thu, 22 Dec 2016 02:47:48: 41000000
INFO @ Thu, 22 Dec 2016 02:47:49: 42000000
INFO @ Thu, 22 Dec 2016 02:47:51: 43000000
INFO @ Thu, 22 Dec 2016 02:47:52: 44000000
INFO @ Thu, 22 Dec 2016 02:47:54: 45000000
INFO @ Thu, 22 Dec 2016 02:47:55: 46000000
INFO @ Thu, 22 Dec 2016 02:47:57: 47000000
INFO @ Thu, 22 Dec 2016 02:47:58: 48000000
INFO @ Thu, 22 Dec 2016 02:48:00: 49000000
INFO @ Thu, 22 Dec 2016 02:48:01: 50000000
INFO @ Thu, 22 Dec 2016 02:48:03: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 02:48:03: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 02:48:03: #1 total tags in treatment: 9914366
INFO @ Thu, 22 Dec 2016 02:48:03: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:48:03: #1 finished!
INFO @ Thu, 22 Dec 2016 02:48:03: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:48:03: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:48:03: #2 Use 135 as fragment length
INFO @ Thu, 22 Dec 2016 02:48:03: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:48:03: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 02:48:03: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:51:27: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 02:55:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 02:55:18: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 02:55:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 02:55:29: Done!
INFO @ Thu, 22 Dec 2016 02:55:52: Read and build treatment bedGraph...
INFO @ Thu, 22 Dec 2016 02:56:13: Read and build control bedGraph...
INFO @ Thu, 22 Dec 2016 02:58:01: Build scoreTrackII...
INFO @ Thu, 22 Dec 2016 02:58:46: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 22 Dec 2016 03:03:24: Write bedGraph of scores...
INFO @ Thu, 22 Dec 2016 03:05:20: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'!
Chromosome KN196487.1 isn't in /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes line 1 of stdin
--------------------Post mortem info--------------------
==============================================================
job_number: 19491
submission_time: Wed Dec 21 14:14:53 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/ZNF519
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/chipseq.bds.20161221_141447_544/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/ZNF519/chipseq.bds.20161221_141447_544/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=50729.ZNF519.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/ZNF519,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 | 19494 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:56 | | End | 2016-12-22 03:35:16 | | Elapsed | 13:20:20 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_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--------------------
13003 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Thu, 22 Dec 2016 03:05:45:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 22 Dec 2016 03:05:45: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:05:45: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:05:47: 1000000
INFO @ Thu, 22 Dec 2016 03:05:49: 2000000
INFO @ Thu, 22 Dec 2016 03:05:51: 3000000
INFO @ Thu, 22 Dec 2016 03:05:53: 4000000
INFO @ Thu, 22 Dec 2016 03:05:55: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:05:56: 1000000
INFO @ Thu, 22 Dec 2016 03:05:58: 2000000
INFO @ Thu, 22 Dec 2016 03:06:00: 3000000
INFO @ Thu, 22 Dec 2016 03:06:02: 4000000
INFO @ Thu, 22 Dec 2016 03:06:03: 5000000
INFO @ Thu, 22 Dec 2016 03:06:05: 6000000
INFO @ Thu, 22 Dec 2016 03:06:07: 7000000
INFO @ Thu, 22 Dec 2016 03:06:08: 8000000
INFO @ Thu, 22 Dec 2016 03:06:10: 9000000
INFO @ Thu, 22 Dec 2016 03:06:12: 10000000
INFO @ Thu, 22 Dec 2016 03:06:14: 11000000
INFO @ Thu, 22 Dec 2016 03:06:15: 12000000
INFO @ Thu, 22 Dec 2016 03:06:17: 13000000
INFO @ Thu, 22 Dec 2016 03:06:19: 14000000
INFO @ Thu, 22 Dec 2016 03:06:20: 15000000
INFO @ Thu, 22 Dec 2016 03:06:22: 16000000
INFO @ Thu, 22 Dec 2016 03:06:24: 17000000
INFO @ Thu, 22 Dec 2016 03:06:25: 18000000
INFO @ Thu, 22 Dec 2016 03:06:27: 19000000
INFO @ Thu, 22 Dec 2016 03:06:29: 20000000
INFO @ Thu, 22 Dec 2016 03:06:30: 21000000
INFO @ Thu, 22 Dec 2016 03:06:32: 22000000
INFO @ Thu, 22 Dec 2016 03:06:34: 23000000
INFO @ Thu, 22 Dec 2016 03:06:36: 24000000
INFO @ Thu, 22 Dec 2016 03:06:37: 25000000
INFO @ Thu, 22 Dec 2016 03:06:39: 26000000
INFO @ Thu, 22 Dec 2016 03:06:41: 27000000
INFO @ Thu, 22 Dec 2016 03:06:42: 28000000
INFO @ Thu, 22 Dec 2016 03:06:44: 29000000
INFO @ Thu, 22 Dec 2016 03:06:46: 30000000
INFO @ Thu, 22 Dec 2016 03:06:48: 31000000
INFO @ Thu, 22 Dec 2016 03:06:49: 32000000
INFO @ Thu, 22 Dec 2016 03:06:51: 33000000
INFO @ Thu, 22 Dec 2016 03:06:53: 34000000
INFO @ Thu, 22 Dec 2016 03:06:54: 35000000
INFO @ Thu, 22 Dec 2016 03:06:56: 36000000
INFO @ Thu, 22 Dec 2016 03:06:58: 37000000
INFO @ Thu, 22 Dec 2016 03:06:59: 38000000
INFO @ Thu, 22 Dec 2016 03:07:01: 39000000
INFO @ Thu, 22 Dec 2016 03:07:03: 40000000
INFO @ Thu, 22 Dec 2016 03:07:05: 41000000
INFO @ Thu, 22 Dec 2016 03:07:06: 42000000
INFO @ Thu, 22 Dec 2016 03:07:08: 43000000
INFO @ Thu, 22 Dec 2016 03:07:10: 44000000
INFO @ Thu, 22 Dec 2016 03:07:11: 45000000
INFO @ Thu, 22 Dec 2016 03:07:13: 46000000
INFO @ Thu, 22 Dec 2016 03:07:15: 47000000
INFO @ Thu, 22 Dec 2016 03:07:16: 48000000
INFO @ Thu, 22 Dec 2016 03:07:18: 49000000
INFO @ Thu, 22 Dec 2016 03:07:20: 50000000
INFO @ Thu, 22 Dec 2016 03:07:22: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 03:07:22: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 03:07:22: #1 total tags in treatment: 4957183
INFO @ Thu, 22 Dec 2016 03:07:22: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:07:22: #1 finished!
INFO @ Thu, 22 Dec 2016 03:07:22: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:07:22: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:07:22: #2 Use 135 as fragment length
INFO @ Thu, 22 Dec 2016 03:07:22: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:07:22: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 03:07:22: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:11:11: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 03:11:11: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 03:11:11: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 03:11:11: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 03:11:11: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:19:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:19:36: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 03:19:37: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 03:19:38: Done!
INFO @ Thu, 22 Dec 2016 03:19:44:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Thu, 22 Dec 2016 03:19:44: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:19:44: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:19:46: 1000000
INFO @ Thu, 22 Dec 2016 03:19:48: 2000000
INFO @ Thu, 22 Dec 2016 03:19:49: 3000000
INFO @ Thu, 22 Dec 2016 03:19:51: 4000000
INFO @ Thu, 22 Dec 2016 03:19:53: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:19:55: 1000000
INFO @ Thu, 22 Dec 2016 03:19:56: 2000000
INFO @ Thu, 22 Dec 2016 03:19:58: 3000000
INFO @ Thu, 22 Dec 2016 03:19:59: 4000000
INFO @ Thu, 22 Dec 2016 03:20:01: 5000000
INFO @ Thu, 22 Dec 2016 03:20:03: 6000000
INFO @ Thu, 22 Dec 2016 03:20:04: 7000000
INFO @ Thu, 22 Dec 2016 03:20:06: 8000000
INFO @ Thu, 22 Dec 2016 03:20:08: 9000000
INFO @ Thu, 22 Dec 2016 03:20:09: 10000000
INFO @ Thu, 22 Dec 2016 03:20:11: 11000000
INFO @ Thu, 22 Dec 2016 03:20:13: 12000000
INFO @ Thu, 22 Dec 2016 03:20:14: 13000000
INFO @ Thu, 22 Dec 2016 03:20:16: 14000000
INFO @ Thu, 22 Dec 2016 03:20:18: 15000000
INFO @ Thu, 22 Dec 2016 03:20:19: 16000000
INFO @ Thu, 22 Dec 2016 03:20:21: 17000000
INFO @ Thu, 22 Dec 2016 03:20:23: 18000000
INFO @ Thu, 22 Dec 2016 03:20:24: 19000000
INFO @ Thu, 22 Dec 2016 03:20:26: 20000000
INFO @ Thu, 22 Dec 2016 03:20:27: 21000000
INFO @ Thu, 22 Dec 2016 03:20:29: 22000000
INFO @ Thu, 22 Dec 2016 03:20:31: 23000000
INFO @ Thu, 22 Dec 2016 03:20:32: 24000000
INFO @ Thu, 22 Dec 2016 03:20:34: 25000000
INFO @ Thu, 22 Dec 2016 03:20:36: 26000000
INFO @ Thu, 22 Dec 2016 03:20:37: 27000000
INFO @ Thu, 22 Dec 2016 03:20:39: 28000000
INFO @ Thu, 22 Dec 2016 03:20:41: 29000000
INFO @ Thu, 22 Dec 2016 03:20:42: 30000000
INFO @ Thu, 22 Dec 2016 03:20:44: 31000000
INFO @ Thu, 22 Dec 2016 03:20:46: 32000000
INFO @ Thu, 22 Dec 2016 03:20:47: 33000000
INFO @ Thu, 22 Dec 2016 03:20:49: 34000000
INFO @ Thu, 22 Dec 2016 03:20:50: 35000000
INFO @ Thu, 22 Dec 2016 03:20:52: 36000000
INFO @ Thu, 22 Dec 2016 03:20:54: 37000000
INFO @ Thu, 22 Dec 2016 03:20:55: 38000000
INFO @ Thu, 22 Dec 2016 03:20:57: 39000000
INFO @ Thu, 22 Dec 2016 03:20:59: 40000000
INFO @ Thu, 22 Dec 2016 03:21:00: 41000000
INFO @ Thu, 22 Dec 2016 03:21:02: 42000000
INFO @ Thu, 22 Dec 2016 03:21:04: 43000000
INFO @ Thu, 22 Dec 2016 03:21:05: 44000000
INFO @ Thu, 22 Dec 2016 03:21:07: 45000000
INFO @ Thu, 22 Dec 2016 03:21:08: 46000000
INFO @ Thu, 22 Dec 2016 03:21:10: 47000000
INFO @ Thu, 22 Dec 2016 03:21:12: 48000000
INFO @ Thu, 22 Dec 2016 03:21:13: 49000000
INFO @ Thu, 22 Dec 2016 03:21:15: 50000000
INFO @ Thu, 22 Dec 2016 03:21:17: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 03:21:17: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 03:21:17: #1 total tags in treatment: 4957183
INFO @ Thu, 22 Dec 2016 03:21:17: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:21:17: #1 finished!
INFO @ Thu, 22 Dec 2016 03:21:17: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:21:17: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:21:17: #2 Use 135 as fragment length
INFO @ Thu, 22 Dec 2016 03:21:17: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:21:17: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 03:21:17: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:26:40: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:34:26: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:34:35: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 03:34:42: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 03:34:48: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 19495 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:57 | | End | 2016-12-22 03:55:54 | | Elapsed | 13:40:56 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_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--------------------
13340 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Thu, 22 Dec 2016 03:22:15:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 22 Dec 2016 03:22:15: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:22:15: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:22:17: 1000000
INFO @ Thu, 22 Dec 2016 03:22:19: 2000000
INFO @ Thu, 22 Dec 2016 03:22:20: 3000000
INFO @ Thu, 22 Dec 2016 03:22:22: 4000000
INFO @ Thu, 22 Dec 2016 03:22:24: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:22:26: 1000000
INFO @ Thu, 22 Dec 2016 03:22:27: 2000000
INFO @ Thu, 22 Dec 2016 03:22:29: 3000000
INFO @ Thu, 22 Dec 2016 03:22:30: 4000000
INFO @ Thu, 22 Dec 2016 03:22:32: 5000000
INFO @ Thu, 22 Dec 2016 03:22:34: 6000000
INFO @ Thu, 22 Dec 2016 03:22:35: 7000000
INFO @ Thu, 22 Dec 2016 03:22:37: 8000000
INFO @ Thu, 22 Dec 2016 03:22:38: 9000000
INFO @ Thu, 22 Dec 2016 03:22:40: 10000000
INFO @ Thu, 22 Dec 2016 03:22:42: 11000000
INFO @ Thu, 22 Dec 2016 03:22:43: 12000000
INFO @ Thu, 22 Dec 2016 03:22:45: 13000000
INFO @ Thu, 22 Dec 2016 03:22:46: 14000000
INFO @ Thu, 22 Dec 2016 03:22:48: 15000000
INFO @ Thu, 22 Dec 2016 03:22:50: 16000000
INFO @ Thu, 22 Dec 2016 03:22:51: 17000000
INFO @ Thu, 22 Dec 2016 03:22:53: 18000000
INFO @ Thu, 22 Dec 2016 03:22:54: 19000000
INFO @ Thu, 22 Dec 2016 03:22:56: 20000000
INFO @ Thu, 22 Dec 2016 03:22:58: 21000000
INFO @ Thu, 22 Dec 2016 03:22:59: 22000000
INFO @ Thu, 22 Dec 2016 03:23:01: 23000000
INFO @ Thu, 22 Dec 2016 03:23:03: 24000000
INFO @ Thu, 22 Dec 2016 03:23:04: 25000000
INFO @ Thu, 22 Dec 2016 03:23:06: 26000000
INFO @ Thu, 22 Dec 2016 03:23:08: 27000000
INFO @ Thu, 22 Dec 2016 03:23:09: 28000000
INFO @ Thu, 22 Dec 2016 03:23:11: 29000000
INFO @ Thu, 22 Dec 2016 03:23:12: 30000000
INFO @ Thu, 22 Dec 2016 03:23:14: 31000000
INFO @ Thu, 22 Dec 2016 03:23:16: 32000000
INFO @ Thu, 22 Dec 2016 03:23:17: 33000000
INFO @ Thu, 22 Dec 2016 03:23:19: 34000000
INFO @ Thu, 22 Dec 2016 03:23:20: 35000000
INFO @ Thu, 22 Dec 2016 03:23:22: 36000000
INFO @ Thu, 22 Dec 2016 03:23:24: 37000000
INFO @ Thu, 22 Dec 2016 03:23:25: 38000000
INFO @ Thu, 22 Dec 2016 03:23:27: 39000000
INFO @ Thu, 22 Dec 2016 03:23:28: 40000000
INFO @ Thu, 22 Dec 2016 03:23:30: 41000000
INFO @ Thu, 22 Dec 2016 03:23:31: 42000000
INFO @ Thu, 22 Dec 2016 03:23:33: 43000000
INFO @ Thu, 22 Dec 2016 03:23:35: 44000000
INFO @ Thu, 22 Dec 2016 03:23:36: 45000000
INFO @ Thu, 22 Dec 2016 03:23:38: 46000000
INFO @ Thu, 22 Dec 2016 03:23:39: 47000000
INFO @ Thu, 22 Dec 2016 03:23:41: 48000000
INFO @ Thu, 22 Dec 2016 03:23:43: 49000000
INFO @ Thu, 22 Dec 2016 03:23:44: 50000000
INFO @ Thu, 22 Dec 2016 03:23:46: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 03:23:46: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 03:23:46: #1 total tags in treatment: 4957183
INFO @ Thu, 22 Dec 2016 03:23:46: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:23:46: #1 finished!
INFO @ Thu, 22 Dec 2016 03:23:46: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:23:46: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:23:46: #2 Use 135 as fragment length
INFO @ Thu, 22 Dec 2016 03:23:46: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:23:46: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 03:23:46: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:30:49: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 03:30:49: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 03:30:49: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 03:30:49: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 03:30:49: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:38:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:38:07: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 03:38:08: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 03:38:09: Done!
INFO @ Thu, 22 Dec 2016 03:38:16:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/pseudo_reps/rep1/pr2/SRR1370893_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 03:38:16: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:38:16: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:38:18: 1000000
INFO @ Thu, 22 Dec 2016 03:38:20: 2000000
INFO @ Thu, 22 Dec 2016 03:38:22: 3000000
INFO @ Thu, 22 Dec 2016 03:38:23: 4000000
INFO @ Thu, 22 Dec 2016 03:38:25: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:38:27: 1000000
INFO @ Thu, 22 Dec 2016 03:38:29: 2000000
INFO @ Thu, 22 Dec 2016 03:38:30: 3000000
INFO @ Thu, 22 Dec 2016 03:38:32: 4000000
INFO @ Thu, 22 Dec 2016 03:38:34: 5000000
INFO @ Thu, 22 Dec 2016 03:38:36: 6000000
INFO @ Thu, 22 Dec 2016 03:38:37: 7000000
INFO @ Thu, 22 Dec 2016 03:38:39: 8000000
INFO @ Thu, 22 Dec 2016 03:38:41: 9000000
INFO @ Thu, 22 Dec 2016 03:38:42: 10000000
INFO @ Thu, 22 Dec 2016 03:38:44: 11000000
INFO @ Thu, 22 Dec 2016 03:38:46: 12000000
INFO @ Thu, 22 Dec 2016 03:38:48: 13000000
INFO @ Thu, 22 Dec 2016 03:38:49: 14000000
INFO @ Thu, 22 Dec 2016 03:38:51: 15000000
INFO @ Thu, 22 Dec 2016 03:38:53: 16000000
INFO @ Thu, 22 Dec 2016 03:38:54: 17000000
INFO @ Thu, 22 Dec 2016 03:38:56: 18000000
INFO @ Thu, 22 Dec 2016 03:38:58: 19000000
INFO @ Thu, 22 Dec 2016 03:38:59: 20000000
INFO @ Thu, 22 Dec 2016 03:39:01: 21000000
INFO @ Thu, 22 Dec 2016 03:39:03: 22000000
INFO @ Thu, 22 Dec 2016 03:39:04: 23000000
INFO @ Thu, 22 Dec 2016 03:39:06: 24000000
INFO @ Thu, 22 Dec 2016 03:39:08: 25000000
INFO @ Thu, 22 Dec 2016 03:39:10: 26000000
INFO @ Thu, 22 Dec 2016 03:39:11: 27000000
INFO @ Thu, 22 Dec 2016 03:39:13: 28000000
INFO @ Thu, 22 Dec 2016 03:39:15: 29000000
INFO @ Thu, 22 Dec 2016 03:39:16: 30000000
INFO @ Thu, 22 Dec 2016 03:39:18: 31000000
INFO @ Thu, 22 Dec 2016 03:39:20: 32000000
INFO @ Thu, 22 Dec 2016 03:39:22: 33000000
INFO @ Thu, 22 Dec 2016 03:39:23: 34000000
INFO @ Thu, 22 Dec 2016 03:39:25: 35000000
INFO @ Thu, 22 Dec 2016 03:39:27: 36000000
INFO @ Thu, 22 Dec 2016 03:39:28: 37000000
INFO @ Thu, 22 Dec 2016 03:39:30: 38000000
INFO @ Thu, 22 Dec 2016 03:39:32: 39000000
INFO @ Thu, 22 Dec 2016 03:39:34: 40000000
INFO @ Thu, 22 Dec 2016 03:39:35: 41000000
INFO @ Thu, 22 Dec 2016 03:39:37: 42000000
INFO @ Thu, 22 Dec 2016 03:39:39: 43000000
INFO @ Thu, 22 Dec 2016 03:39:40: 44000000
INFO @ Thu, 22 Dec 2016 03:39:42: 45000000
INFO @ Thu, 22 Dec 2016 03:39:44: 46000000
INFO @ Thu, 22 Dec 2016 03:39:45: 47000000
INFO @ Thu, 22 Dec 2016 03:39:47: 48000000
INFO @ Thu, 22 Dec 2016 03:39:49: 49000000
INFO @ Thu, 22 Dec 2016 03:39:50: 50000000
INFO @ Thu, 22 Dec 2016 03:39:52: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 03:39:52: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 03:39:52: #1 total tags in treatment: 4957183
INFO @ Thu, 22 Dec 2016 03:39:52: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:39:52: #1 finished!
INFO @ Thu, 22 Dec 2016 03:39:52: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:39:52: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:39:52: #2 Use 135 as fragment length
INFO @ Thu, 22 Dec 2016 03:39:52: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:39:52: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 03:39:52: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:47:18: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:55:02: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:55:11: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 03:55:18: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 03:55:24: Done!
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