| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 19485 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:22 | | End | 2016-12-21 14:14:22 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/signal/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/signal/macs2/rep1/SRR1370888_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/ZNF273/out/align/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/align/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1 -o "SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/signal/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/align/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1 -o "SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/signal/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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--------------------
10586 (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 01:28:29:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/rep1/SRR1370888_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 01:28:29: #1 read tag files...
INFO @ Thu, 22 Dec 2016 01:28:29: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 01:28:31: 1000000
INFO @ Thu, 22 Dec 2016 01:28:33: 2000000
INFO @ Thu, 22 Dec 2016 01:28:34: 3000000
INFO @ Thu, 22 Dec 2016 01:28:36: 4000000
INFO @ Thu, 22 Dec 2016 01:28:38: 5000000
INFO @ Thu, 22 Dec 2016 01:28:39: 6000000
INFO @ Thu, 22 Dec 2016 01:28:41: 7000000
INFO @ Thu, 22 Dec 2016 01:28:42: 8000000
INFO @ Thu, 22 Dec 2016 01:28:44: 9000000
INFO @ Thu, 22 Dec 2016 01:28:45: 10000000
INFO @ Thu, 22 Dec 2016 01:28:47: 11000000
INFO @ Thu, 22 Dec 2016 01:28:49: 12000000
INFO @ Thu, 22 Dec 2016 01:28:50: 13000000
INFO @ Thu, 22 Dec 2016 01:28:52: 14000000
INFO @ Thu, 22 Dec 2016 01:28:53: 15000000
INFO @ Thu, 22 Dec 2016 01:28:55: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 01:28:57: 1000000
INFO @ Thu, 22 Dec 2016 01:28:59: 2000000
INFO @ Thu, 22 Dec 2016 01:29:00: 3000000
INFO @ Thu, 22 Dec 2016 01:29:02: 4000000
INFO @ Thu, 22 Dec 2016 01:29:03: 5000000
INFO @ Thu, 22 Dec 2016 01:29:05: 6000000
INFO @ Thu, 22 Dec 2016 01:29:07: 7000000
INFO @ Thu, 22 Dec 2016 01:29:08: 8000000
INFO @ Thu, 22 Dec 2016 01:29:10: 9000000
INFO @ Thu, 22 Dec 2016 01:29:11: 10000000
INFO @ Thu, 22 Dec 2016 01:29:13: 11000000
INFO @ Thu, 22 Dec 2016 01:29:15: 12000000
INFO @ Thu, 22 Dec 2016 01:29:16: 13000000
INFO @ Thu, 22 Dec 2016 01:29:18: 14000000
INFO @ Thu, 22 Dec 2016 01:29:19: 15000000
INFO @ Thu, 22 Dec 2016 01:29:21: 16000000
INFO @ Thu, 22 Dec 2016 01:29:23: 17000000
INFO @ Thu, 22 Dec 2016 01:29:24: 18000000
INFO @ Thu, 22 Dec 2016 01:29:26: 19000000
INFO @ Thu, 22 Dec 2016 01:29:28: 20000000
INFO @ Thu, 22 Dec 2016 01:29:29: 21000000
INFO @ Thu, 22 Dec 2016 01:29:31: 22000000
INFO @ Thu, 22 Dec 2016 01:29:32: 23000000
INFO @ Thu, 22 Dec 2016 01:29:34: 24000000
INFO @ Thu, 22 Dec 2016 01:29:36: 25000000
INFO @ Thu, 22 Dec 2016 01:29:37: 26000000
INFO @ Thu, 22 Dec 2016 01:29:39: 27000000
INFO @ Thu, 22 Dec 2016 01:29:40: 28000000
INFO @ Thu, 22 Dec 2016 01:29:42: 29000000
INFO @ Thu, 22 Dec 2016 01:29:43: 30000000
INFO @ Thu, 22 Dec 2016 01:29:45: 31000000
INFO @ Thu, 22 Dec 2016 01:29:47: 32000000
INFO @ Thu, 22 Dec 2016 01:29:49: 33000000
INFO @ Thu, 22 Dec 2016 01:29:50: 34000000
INFO @ Thu, 22 Dec 2016 01:29:52: 35000000
INFO @ Thu, 22 Dec 2016 01:29:54: 36000000
INFO @ Thu, 22 Dec 2016 01:29:55: 37000000
INFO @ Thu, 22 Dec 2016 01:29:57: 38000000
INFO @ Thu, 22 Dec 2016 01:29:58: 39000000
INFO @ Thu, 22 Dec 2016 01:30:00: 40000000
INFO @ Thu, 22 Dec 2016 01:30:02: 41000000
INFO @ Thu, 22 Dec 2016 01:30:03: 42000000
INFO @ Thu, 22 Dec 2016 01:30:05: 43000000
INFO @ Thu, 22 Dec 2016 01:30:06: 44000000
INFO @ Thu, 22 Dec 2016 01:30:08: 45000000
INFO @ Thu, 22 Dec 2016 01:30:10: 46000000
INFO @ Thu, 22 Dec 2016 01:30:11: 47000000
INFO @ Thu, 22 Dec 2016 01:30:13: 48000000
INFO @ Thu, 22 Dec 2016 01:30:14: 49000000
INFO @ Thu, 22 Dec 2016 01:30:16: 50000000
INFO @ Thu, 22 Dec 2016 01:30:18: #1 tag size is determined as 49 bps
INFO @ Thu, 22 Dec 2016 01:30:18: #1 tag size = 49
INFO @ Thu, 22 Dec 2016 01:30:18: #1 total tags in treatment: 15988029
INFO @ Thu, 22 Dec 2016 01:30:18: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 01:30:18: #1 finished!
INFO @ Thu, 22 Dec 2016 01:30:18: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 01:30:18: #2 Skipped...
INFO @ Thu, 22 Dec 2016 01:30:18: #2 Use 150 as fragment length
INFO @ Thu, 22 Dec 2016 01:30:18: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 01:30:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 01:30:18: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 01:33:55: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 01:33:55: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 01:33:55: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 01:33:55: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 01:33:55: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 01:39:38: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 01:39:39: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 01:39:39: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 01:39:40: Done!
INFO @ Thu, 22 Dec 2016 01:39:44:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_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/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/rep1/SRR1370888_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 01:39:44: #1 read tag files...
INFO @ Thu, 22 Dec 2016 01:39:44: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 01:39:45: 1000000
INFO @ Thu, 22 Dec 2016 01:39:47: 2000000
INFO @ Thu, 22 Dec 2016 01:39:48: 3000000
INFO @ Thu, 22 Dec 2016 01:39:50: 4000000
INFO @ Thu, 22 Dec 2016 01:39:51: 5000000
INFO @ Thu, 22 Dec 2016 01:39:53: 6000000
INFO @ Thu, 22 Dec 2016 01:39:54: 7000000
INFO @ Thu, 22 Dec 2016 01:39:56: 8000000
INFO @ Thu, 22 Dec 2016 01:39:58: 9000000
INFO @ Thu, 22 Dec 2016 01:39:59: 10000000
INFO @ Thu, 22 Dec 2016 01:40:01: 11000000
INFO @ Thu, 22 Dec 2016 01:40:02: 12000000
INFO @ Thu, 22 Dec 2016 01:40:04: 13000000
INFO @ Thu, 22 Dec 2016 01:40:05: 14000000
INFO @ Thu, 22 Dec 2016 01:40:07: 15000000
INFO @ Thu, 22 Dec 2016 01:40:09: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 01:40:11: 1000000
INFO @ Thu, 22 Dec 2016 01:40:12: 2000000
INFO @ Thu, 22 Dec 2016 01:40:14: 3000000
INFO @ Thu, 22 Dec 2016 01:40:15: 4000000
INFO @ Thu, 22 Dec 2016 01:40:17: 5000000
INFO @ Thu, 22 Dec 2016 01:40:19: 6000000
INFO @ Thu, 22 Dec 2016 01:40:20: 7000000
INFO @ Thu, 22 Dec 2016 01:40:22: 8000000
INFO @ Thu, 22 Dec 2016 01:40:23: 9000000
INFO @ Thu, 22 Dec 2016 01:40:25: 10000000
INFO @ Thu, 22 Dec 2016 01:40:27: 11000000
INFO @ Thu, 22 Dec 2016 01:40:28: 12000000
INFO @ Thu, 22 Dec 2016 01:40:30: 13000000
INFO @ Thu, 22 Dec 2016 01:40:31: 14000000
INFO @ Thu, 22 Dec 2016 01:40:33: 15000000
INFO @ Thu, 22 Dec 2016 01:40:35: 16000000
INFO @ Thu, 22 Dec 2016 01:40:36: 17000000
INFO @ Thu, 22 Dec 2016 01:40:38: 18000000
INFO @ Thu, 22 Dec 2016 01:40:40: 19000000
INFO @ Thu, 22 Dec 2016 01:40:41: 20000000
INFO @ Thu, 22 Dec 2016 01:40:43: 21000000
INFO @ Thu, 22 Dec 2016 01:40:44: 22000000
INFO @ Thu, 22 Dec 2016 01:40:46: 23000000
INFO @ Thu, 22 Dec 2016 01:40:47: 24000000
INFO @ Thu, 22 Dec 2016 01:40:49: 25000000
INFO @ Thu, 22 Dec 2016 01:40:51: 26000000
INFO @ Thu, 22 Dec 2016 01:40:52: 27000000
INFO @ Thu, 22 Dec 2016 01:40:54: 28000000
INFO @ Thu, 22 Dec 2016 01:40:56: 29000000
INFO @ Thu, 22 Dec 2016 01:40:57: 30000000
INFO @ Thu, 22 Dec 2016 01:40:59: 31000000
INFO @ Thu, 22 Dec 2016 01:41:01: 32000000
INFO @ Thu, 22 Dec 2016 01:41:02: 33000000
INFO @ Thu, 22 Dec 2016 01:41:04: 34000000
INFO @ Thu, 22 Dec 2016 01:41:05: 35000000
INFO @ Thu, 22 Dec 2016 01:41:07: 36000000
INFO @ Thu, 22 Dec 2016 01:41:09: 37000000
INFO @ Thu, 22 Dec 2016 01:41:10: 38000000
INFO @ Thu, 22 Dec 2016 01:41:12: 39000000
INFO @ Thu, 22 Dec 2016 01:41:13: 40000000
INFO @ Thu, 22 Dec 2016 01:41:15: 41000000
INFO @ Thu, 22 Dec 2016 01:41:17: 42000000
INFO @ Thu, 22 Dec 2016 01:41:18: 43000000
INFO @ Thu, 22 Dec 2016 01:41:20: 44000000
INFO @ Thu, 22 Dec 2016 01:41:21: 45000000
INFO @ Thu, 22 Dec 2016 01:41:23: 46000000
INFO @ Thu, 22 Dec 2016 01:41:25: 47000000
INFO @ Thu, 22 Dec 2016 01:41:26: 48000000
INFO @ Thu, 22 Dec 2016 01:41:28: 49000000
INFO @ Thu, 22 Dec 2016 01:41:29: 50000000
INFO @ Thu, 22 Dec 2016 01:41:31: #1 tag size is determined as 49 bps
INFO @ Thu, 22 Dec 2016 01:41:31: #1 tag size = 49
INFO @ Thu, 22 Dec 2016 01:41:31: #1 total tags in treatment: 15988029
INFO @ Thu, 22 Dec 2016 01:41:31: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 01:41:31: #1 finished!
INFO @ Thu, 22 Dec 2016 01:41:31: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 01:41:31: #2 Skipped...
INFO @ Thu, 22 Dec 2016 01:41:31: #2 Use 150 as fragment length
INFO @ Thu, 22 Dec 2016 01:41:31: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 01:41:31: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 01:41:31: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 01:44:54: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 01:48:16: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 01:48:23: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 01:48:27: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 01:48:32: Done!
INFO @ Thu, 22 Dec 2016 01:48:49: Read and build treatment bedGraph...
INFO @ Thu, 22 Dec 2016 01:49:22: Read and build control bedGraph...
INFO @ Thu, 22 Dec 2016 01:51:13: Build scoreTrackII...
INFO @ Thu, 22 Dec 2016 01:52:04: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 22 Dec 2016 01:57:08: Write bedGraph of scores...
INFO @ Thu, 22 Dec 2016 02:00:07: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/rep1/SRR1370888_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: 19485
exec_file: job_scripts/19485
submission_time: Wed Dec 21 14:14:22 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/ZNF273
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/chipseq.bds.20161221_141415_748/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/ZNF273/chipseq.bds.20161221_141415_748/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=48736.ZNF273.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/ZNF273,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
script_file: STDIN
usage 1: cpu=00:31:32, mem=3289.42600 GBs, io=49.79497, vmem=294.328M, maxvmem=3.948G
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 | 19486 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:25 | | End | 2016-12-22 02:20:07 | | Elapsed | 12:05:41 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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--------------------
11147 (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 02:00:29:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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 02:00:29: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:00:29: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:00:31: 1000000
INFO @ Thu, 22 Dec 2016 02:00:33: 2000000
INFO @ Thu, 22 Dec 2016 02:00:35: 3000000
INFO @ Thu, 22 Dec 2016 02:00:37: 4000000
INFO @ Thu, 22 Dec 2016 02:00:38: 5000000
INFO @ Thu, 22 Dec 2016 02:00:40: 6000000
INFO @ Thu, 22 Dec 2016 02:00:42: 7000000
INFO @ Thu, 22 Dec 2016 02:00:44: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:00:46: 1000000
INFO @ Thu, 22 Dec 2016 02:00:47: 2000000
INFO @ Thu, 22 Dec 2016 02:00:49: 3000000
INFO @ Thu, 22 Dec 2016 02:00:51: 4000000
INFO @ Thu, 22 Dec 2016 02:00:53: 5000000
INFO @ Thu, 22 Dec 2016 02:00:54: 6000000
INFO @ Thu, 22 Dec 2016 02:00:56: 7000000
INFO @ Thu, 22 Dec 2016 02:00:58: 8000000
INFO @ Thu, 22 Dec 2016 02:00:59: 9000000
INFO @ Thu, 22 Dec 2016 02:01:01: 10000000
INFO @ Thu, 22 Dec 2016 02:01:03: 11000000
INFO @ Thu, 22 Dec 2016 02:01:04: 12000000
INFO @ Thu, 22 Dec 2016 02:01:06: 13000000
INFO @ Thu, 22 Dec 2016 02:01:08: 14000000
INFO @ Thu, 22 Dec 2016 02:01:09: 15000000
INFO @ Thu, 22 Dec 2016 02:01:11: 16000000
INFO @ Thu, 22 Dec 2016 02:01:13: 17000000
INFO @ Thu, 22 Dec 2016 02:01:14: 18000000
INFO @ Thu, 22 Dec 2016 02:01:16: 19000000
INFO @ Thu, 22 Dec 2016 02:01:18: 20000000
INFO @ Thu, 22 Dec 2016 02:01:19: 21000000
INFO @ Thu, 22 Dec 2016 02:01:21: 22000000
INFO @ Thu, 22 Dec 2016 02:01:23: 23000000
INFO @ Thu, 22 Dec 2016 02:01:24: 24000000
INFO @ Thu, 22 Dec 2016 02:01:26: 25000000
INFO @ Thu, 22 Dec 2016 02:01:28: 26000000
INFO @ Thu, 22 Dec 2016 02:01:29: 27000000
INFO @ Thu, 22 Dec 2016 02:01:31: 28000000
INFO @ Thu, 22 Dec 2016 02:01:33: 29000000
INFO @ Thu, 22 Dec 2016 02:01:34: 30000000
INFO @ Thu, 22 Dec 2016 02:01:36: 31000000
INFO @ Thu, 22 Dec 2016 02:01:38: 32000000
INFO @ Thu, 22 Dec 2016 02:01:39: 33000000
INFO @ Thu, 22 Dec 2016 02:01:41: 34000000
INFO @ Thu, 22 Dec 2016 02:01:42: 35000000
INFO @ Thu, 22 Dec 2016 02:01:44: 36000000
INFO @ Thu, 22 Dec 2016 02:01:46: 37000000
INFO @ Thu, 22 Dec 2016 02:01:48: 38000000
INFO @ Thu, 22 Dec 2016 02:01:49: 39000000
INFO @ Thu, 22 Dec 2016 02:01:51: 40000000
INFO @ Thu, 22 Dec 2016 02:01:52: 41000000
INFO @ Thu, 22 Dec 2016 02:01:54: 42000000
INFO @ Thu, 22 Dec 2016 02:01:56: 43000000
INFO @ Thu, 22 Dec 2016 02:01:57: 44000000
INFO @ Thu, 22 Dec 2016 02:01:59: 45000000
INFO @ Thu, 22 Dec 2016 02:02:01: 46000000
INFO @ Thu, 22 Dec 2016 02:02:02: 47000000
INFO @ Thu, 22 Dec 2016 02:02:04: 48000000
INFO @ Thu, 22 Dec 2016 02:02:06: 49000000
INFO @ Thu, 22 Dec 2016 02:02:07: 50000000
INFO @ Thu, 22 Dec 2016 02:02:09: #1 tag size is determined as 49 bps
INFO @ Thu, 22 Dec 2016 02:02:09: #1 tag size = 49
INFO @ Thu, 22 Dec 2016 02:02:09: #1 total tags in treatment: 7994015
INFO @ Thu, 22 Dec 2016 02:02:09: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:02:09: #1 finished!
INFO @ Thu, 22 Dec 2016 02:02:09: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:02:09: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:02:09: #2 Use 150 as fragment length
INFO @ Thu, 22 Dec 2016 02:02:09: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:02:09: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 02:02:09: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:05:37: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 02:05:37: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 02:05:37: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 02:05:37: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 02:05:37: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 02:10:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 02:10:29: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 02:10:30: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 02:10:30: Done!
INFO @ Thu, 22 Dec 2016 02:10:34:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr1/SRR1370888_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 02:10:34: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:10:34: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:10:36: 1000000
INFO @ Thu, 22 Dec 2016 02:10:38: 2000000
INFO @ Thu, 22 Dec 2016 02:10:40: 3000000
INFO @ Thu, 22 Dec 2016 02:10:41: 4000000
INFO @ Thu, 22 Dec 2016 02:10:43: 5000000
INFO @ Thu, 22 Dec 2016 02:10:45: 6000000
INFO @ Thu, 22 Dec 2016 02:10:47: 7000000
INFO @ Thu, 22 Dec 2016 02:10:49: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:10:51: 1000000
INFO @ Thu, 22 Dec 2016 02:10:53: 2000000
INFO @ Thu, 22 Dec 2016 02:10:55: 3000000
INFO @ Thu, 22 Dec 2016 02:10:57: 4000000
INFO @ Thu, 22 Dec 2016 02:10:59: 5000000
INFO @ Thu, 22 Dec 2016 02:11:00: 6000000
INFO @ Thu, 22 Dec 2016 02:11:02: 7000000
INFO @ Thu, 22 Dec 2016 02:11:04: 8000000
INFO @ Thu, 22 Dec 2016 02:11:06: 9000000
INFO @ Thu, 22 Dec 2016 02:11:07: 10000000
INFO @ Thu, 22 Dec 2016 02:11:09: 11000000
INFO @ Thu, 22 Dec 2016 02:11:11: 12000000
INFO @ Thu, 22 Dec 2016 02:11:13: 13000000
INFO @ Thu, 22 Dec 2016 02:11:15: 14000000
INFO @ Thu, 22 Dec 2016 02:11:17: 15000000
INFO @ Thu, 22 Dec 2016 02:11:18: 16000000
INFO @ Thu, 22 Dec 2016 02:11:20: 17000000
INFO @ Thu, 22 Dec 2016 02:11:22: 18000000
INFO @ Thu, 22 Dec 2016 02:11:24: 19000000
INFO @ Thu, 22 Dec 2016 02:11:26: 20000000
INFO @ Thu, 22 Dec 2016 02:11:27: 21000000
INFO @ Thu, 22 Dec 2016 02:11:29: 22000000
INFO @ Thu, 22 Dec 2016 02:11:31: 23000000
INFO @ Thu, 22 Dec 2016 02:11:33: 24000000
INFO @ Thu, 22 Dec 2016 02:11:34: 25000000
INFO @ Thu, 22 Dec 2016 02:11:36: 26000000
INFO @ Thu, 22 Dec 2016 02:11:38: 27000000
INFO @ Thu, 22 Dec 2016 02:11:40: 28000000
INFO @ Thu, 22 Dec 2016 02:11:42: 29000000
INFO @ Thu, 22 Dec 2016 02:11:43: 30000000
INFO @ Thu, 22 Dec 2016 02:11:45: 31000000
INFO @ Thu, 22 Dec 2016 02:11:47: 32000000
INFO @ Thu, 22 Dec 2016 02:11:49: 33000000
INFO @ Thu, 22 Dec 2016 02:11:51: 34000000
INFO @ Thu, 22 Dec 2016 02:11:53: 35000000
INFO @ Thu, 22 Dec 2016 02:11:54: 36000000
INFO @ Thu, 22 Dec 2016 02:11:56: 37000000
INFO @ Thu, 22 Dec 2016 02:11:58: 38000000
INFO @ Thu, 22 Dec 2016 02:12:00: 39000000
INFO @ Thu, 22 Dec 2016 02:12:02: 40000000
INFO @ Thu, 22 Dec 2016 02:12:03: 41000000
INFO @ Thu, 22 Dec 2016 02:12:05: 42000000
INFO @ Thu, 22 Dec 2016 02:12:07: 43000000
INFO @ Thu, 22 Dec 2016 02:12:09: 44000000
INFO @ Thu, 22 Dec 2016 02:12:10: 45000000
INFO @ Thu, 22 Dec 2016 02:12:12: 46000000
INFO @ Thu, 22 Dec 2016 02:12:14: 47000000
INFO @ Thu, 22 Dec 2016 02:12:16: 48000000
INFO @ Thu, 22 Dec 2016 02:12:18: 49000000
INFO @ Thu, 22 Dec 2016 02:12:19: 50000000
INFO @ Thu, 22 Dec 2016 02:12:21: #1 tag size is determined as 49 bps
INFO @ Thu, 22 Dec 2016 02:12:21: #1 tag size = 49
INFO @ Thu, 22 Dec 2016 02:12:21: #1 total tags in treatment: 7994015
INFO @ Thu, 22 Dec 2016 02:12:21: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:12:21: #1 finished!
INFO @ Thu, 22 Dec 2016 02:12:21: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:12:21: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:12:21: #2 Use 150 as fragment length
INFO @ Thu, 22 Dec 2016 02:12:21: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:12:21: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 02:12:21: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:15:55: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 02:19:32: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 02:19:39: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 02:19:43: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 02:19:48: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 19487 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:26 | | End | 2016-12-22 02:28:38 | | Elapsed | 12:14:11 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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--------------------
11279 (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 02:07:00:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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 02:07:00: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:07:00: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:07:02: 1000000
INFO @ Thu, 22 Dec 2016 02:07:04: 2000000
INFO @ Thu, 22 Dec 2016 02:07:06: 3000000
INFO @ Thu, 22 Dec 2016 02:07:07: 4000000
INFO @ Thu, 22 Dec 2016 02:07:09: 5000000
INFO @ Thu, 22 Dec 2016 02:07:11: 6000000
INFO @ Thu, 22 Dec 2016 02:07:13: 7000000
INFO @ Thu, 22 Dec 2016 02:07:15: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:07:16: 1000000
INFO @ Thu, 22 Dec 2016 02:07:18: 2000000
INFO @ Thu, 22 Dec 2016 02:07:20: 3000000
INFO @ Thu, 22 Dec 2016 02:07:21: 4000000
INFO @ Thu, 22 Dec 2016 02:07:23: 5000000
INFO @ Thu, 22 Dec 2016 02:07:25: 6000000
INFO @ Thu, 22 Dec 2016 02:07:26: 7000000
INFO @ Thu, 22 Dec 2016 02:07:28: 8000000
INFO @ Thu, 22 Dec 2016 02:07:29: 9000000
INFO @ Thu, 22 Dec 2016 02:07:31: 10000000
INFO @ Thu, 22 Dec 2016 02:07:33: 11000000
INFO @ Thu, 22 Dec 2016 02:07:34: 12000000
INFO @ Thu, 22 Dec 2016 02:07:36: 13000000
INFO @ Thu, 22 Dec 2016 02:07:37: 14000000
INFO @ Thu, 22 Dec 2016 02:07:39: 15000000
INFO @ Thu, 22 Dec 2016 02:07:41: 16000000
INFO @ Thu, 22 Dec 2016 02:07:42: 17000000
INFO @ Thu, 22 Dec 2016 02:07:44: 18000000
INFO @ Thu, 22 Dec 2016 02:07:46: 19000000
INFO @ Thu, 22 Dec 2016 02:07:48: 20000000
INFO @ Thu, 22 Dec 2016 02:07:49: 21000000
INFO @ Thu, 22 Dec 2016 02:07:51: 22000000
INFO @ Thu, 22 Dec 2016 02:07:52: 23000000
INFO @ Thu, 22 Dec 2016 02:07:54: 24000000
INFO @ Thu, 22 Dec 2016 02:07:56: 25000000
INFO @ Thu, 22 Dec 2016 02:07:57: 26000000
INFO @ Thu, 22 Dec 2016 02:07:59: 27000000
INFO @ Thu, 22 Dec 2016 02:08:01: 28000000
INFO @ Thu, 22 Dec 2016 02:08:02: 29000000
INFO @ Thu, 22 Dec 2016 02:08:04: 30000000
INFO @ Thu, 22 Dec 2016 02:08:05: 31000000
INFO @ Thu, 22 Dec 2016 02:08:07: 32000000
INFO @ Thu, 22 Dec 2016 02:08:09: 33000000
INFO @ Thu, 22 Dec 2016 02:08:10: 34000000
INFO @ Thu, 22 Dec 2016 02:08:12: 35000000
INFO @ Thu, 22 Dec 2016 02:08:13: 36000000
INFO @ Thu, 22 Dec 2016 02:08:15: 37000000
INFO @ Thu, 22 Dec 2016 02:08:17: 38000000
INFO @ Thu, 22 Dec 2016 02:08:18: 39000000
INFO @ Thu, 22 Dec 2016 02:08:20: 40000000
INFO @ Thu, 22 Dec 2016 02:08:22: 41000000
INFO @ Thu, 22 Dec 2016 02:08:23: 42000000
INFO @ Thu, 22 Dec 2016 02:08:25: 43000000
INFO @ Thu, 22 Dec 2016 02:08:26: 44000000
INFO @ Thu, 22 Dec 2016 02:08:28: 45000000
INFO @ Thu, 22 Dec 2016 02:08:30: 46000000
INFO @ Thu, 22 Dec 2016 02:08:31: 47000000
INFO @ Thu, 22 Dec 2016 02:08:33: 48000000
INFO @ Thu, 22 Dec 2016 02:08:34: 49000000
INFO @ Thu, 22 Dec 2016 02:08:36: 50000000
INFO @ Thu, 22 Dec 2016 02:08:38: #1 tag size is determined as 50 bps
INFO @ Thu, 22 Dec 2016 02:08:38: #1 tag size = 50
INFO @ Thu, 22 Dec 2016 02:08:38: #1 total tags in treatment: 7994014
INFO @ Thu, 22 Dec 2016 02:08:38: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:08:38: #1 finished!
INFO @ Thu, 22 Dec 2016 02:08:38: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:08:38: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:08:38: #2 Use 150 as fragment length
INFO @ Thu, 22 Dec 2016 02:08:38: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:08:38: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 02:08:38: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:12:21: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 02:12:21: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 02:12:21: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 02:12:21: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 02:12:21: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 02:18:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 02:18:35: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 02:18:35: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 02:18:35: Done!
INFO @ Thu, 22 Dec 2016 02:18:39:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_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/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/align/pseudo_reps/rep1/pr2/SRR1370888_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 02:18:39: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:18:39: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:18:41: 1000000
INFO @ Thu, 22 Dec 2016 02:18:42: 2000000
INFO @ Thu, 22 Dec 2016 02:18:44: 3000000
INFO @ Thu, 22 Dec 2016 02:18:46: 4000000
INFO @ Thu, 22 Dec 2016 02:18:47: 5000000
INFO @ Thu, 22 Dec 2016 02:18:49: 6000000
INFO @ Thu, 22 Dec 2016 02:18:51: 7000000
INFO @ Thu, 22 Dec 2016 02:18:53: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:18:54: 1000000
INFO @ Thu, 22 Dec 2016 02:18:56: 2000000
INFO @ Thu, 22 Dec 2016 02:18:58: 3000000
INFO @ Thu, 22 Dec 2016 02:18:59: 4000000
INFO @ Thu, 22 Dec 2016 02:19:01: 5000000
INFO @ Thu, 22 Dec 2016 02:19:02: 6000000
INFO @ Thu, 22 Dec 2016 02:19:04: 7000000
INFO @ Thu, 22 Dec 2016 02:19:05: 8000000
INFO @ Thu, 22 Dec 2016 02:19:07: 9000000
INFO @ Thu, 22 Dec 2016 02:19:08: 10000000
INFO @ Thu, 22 Dec 2016 02:19:10: 11000000
INFO @ Thu, 22 Dec 2016 02:19:12: 12000000
INFO @ Thu, 22 Dec 2016 02:19:13: 13000000
INFO @ Thu, 22 Dec 2016 02:19:15: 14000000
INFO @ Thu, 22 Dec 2016 02:19:16: 15000000
INFO @ Thu, 22 Dec 2016 02:19:18: 16000000
INFO @ Thu, 22 Dec 2016 02:19:19: 17000000
INFO @ Thu, 22 Dec 2016 02:19:21: 18000000
INFO @ Thu, 22 Dec 2016 02:19:22: 19000000
INFO @ Thu, 22 Dec 2016 02:19:24: 20000000
INFO @ Thu, 22 Dec 2016 02:19:26: 21000000
INFO @ Thu, 22 Dec 2016 02:19:27: 22000000
INFO @ Thu, 22 Dec 2016 02:19:29: 23000000
INFO @ Thu, 22 Dec 2016 02:19:30: 24000000
INFO @ Thu, 22 Dec 2016 02:19:32: 25000000
INFO @ Thu, 22 Dec 2016 02:19:33: 26000000
INFO @ Thu, 22 Dec 2016 02:19:35: 27000000
INFO @ Thu, 22 Dec 2016 02:19:36: 28000000
INFO @ Thu, 22 Dec 2016 02:19:38: 29000000
INFO @ Thu, 22 Dec 2016 02:19:40: 30000000
INFO @ Thu, 22 Dec 2016 02:19:41: 31000000
INFO @ Thu, 22 Dec 2016 02:19:43: 32000000
INFO @ Thu, 22 Dec 2016 02:19:44: 33000000
INFO @ Thu, 22 Dec 2016 02:19:46: 34000000
INFO @ Thu, 22 Dec 2016 02:19:48: 35000000
INFO @ Thu, 22 Dec 2016 02:19:49: 36000000
INFO @ Thu, 22 Dec 2016 02:19:51: 37000000
INFO @ Thu, 22 Dec 2016 02:19:53: 38000000
INFO @ Thu, 22 Dec 2016 02:19:54: 39000000
INFO @ Thu, 22 Dec 2016 02:19:56: 40000000
INFO @ Thu, 22 Dec 2016 02:19:57: 41000000
INFO @ Thu, 22 Dec 2016 02:19:59: 42000000
INFO @ Thu, 22 Dec 2016 02:20:00: 43000000
INFO @ Thu, 22 Dec 2016 02:20:02: 44000000
INFO @ Thu, 22 Dec 2016 02:20:04: 45000000
INFO @ Thu, 22 Dec 2016 02:20:05: 46000000
INFO @ Thu, 22 Dec 2016 02:20:07: 47000000
INFO @ Thu, 22 Dec 2016 02:20:08: 48000000
INFO @ Thu, 22 Dec 2016 02:20:10: 49000000
INFO @ Thu, 22 Dec 2016 02:20:12: 50000000
INFO @ Thu, 22 Dec 2016 02:20:13: #1 tag size is determined as 50 bps
INFO @ Thu, 22 Dec 2016 02:20:13: #1 tag size = 50
INFO @ Thu, 22 Dec 2016 02:20:13: #1 total tags in treatment: 7994014
INFO @ Thu, 22 Dec 2016 02:20:13: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:20:13: #1 finished!
INFO @ Thu, 22 Dec 2016 02:20:13: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:20:13: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:20:13: #2 Use 150 as fragment length
INFO @ Thu, 22 Dec 2016 02:20:13: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:20:13: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 02:20:13: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:24:21: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 02:28:03: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 02:28:10: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 02:28:14: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF273/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 02:28:19: Done!
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