| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 19492 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:54 | | End | 2016-12-21 14:14:54 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/signal/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/signal/macs2/rep1/SRR1370912_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/ZNF653/out/align/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/align/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1 -o "SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/signal/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/align/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1 -o "SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/signal/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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--------------------
12451 (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 02:39:14:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/rep1/SRR1370912_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 02:39:14: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:39:14: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:39:16: 1000000
INFO @ Thu, 22 Dec 2016 02:39:18: 2000000
INFO @ Thu, 22 Dec 2016 02:39:19: 3000000
INFO @ Thu, 22 Dec 2016 02:39:21: 4000000
INFO @ Thu, 22 Dec 2016 02:39:22: 5000000
INFO @ Thu, 22 Dec 2016 02:39:24: 6000000
INFO @ Thu, 22 Dec 2016 02:39:26: 7000000
INFO @ Thu, 22 Dec 2016 02:39:27: 8000000
INFO @ Thu, 22 Dec 2016 02:39:29: 9000000
INFO @ Thu, 22 Dec 2016 02:39:30: 10000000
INFO @ Thu, 22 Dec 2016 02:39:32: 11000000
INFO @ Thu, 22 Dec 2016 02:39:33: 12000000
INFO @ Thu, 22 Dec 2016 02:39:35: 13000000
INFO @ Thu, 22 Dec 2016 02:39:37: 14000000
INFO @ Thu, 22 Dec 2016 02:39:38: 15000000
INFO @ Thu, 22 Dec 2016 02:39:40: 16000000
INFO @ Thu, 22 Dec 2016 02:39:41: 17000000
INFO @ Thu, 22 Dec 2016 02:39:43: 18000000
INFO @ Thu, 22 Dec 2016 02:39:43: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:39:45: 1000000
INFO @ Thu, 22 Dec 2016 02:39:46: 2000000
INFO @ Thu, 22 Dec 2016 02:39:48: 3000000
INFO @ Thu, 22 Dec 2016 02:39:50: 4000000
INFO @ Thu, 22 Dec 2016 02:39:51: 5000000
INFO @ Thu, 22 Dec 2016 02:39:53: 6000000
INFO @ Thu, 22 Dec 2016 02:39:54: 7000000
INFO @ Thu, 22 Dec 2016 02:39:56: 8000000
INFO @ Thu, 22 Dec 2016 02:39:58: 9000000
INFO @ Thu, 22 Dec 2016 02:39:59: 10000000
INFO @ Thu, 22 Dec 2016 02:40:01: 11000000
INFO @ Thu, 22 Dec 2016 02:40:03: 12000000
INFO @ Thu, 22 Dec 2016 02:40:04: 13000000
INFO @ Thu, 22 Dec 2016 02:40:06: 14000000
INFO @ Thu, 22 Dec 2016 02:40:08: 15000000
INFO @ Thu, 22 Dec 2016 02:40:09: 16000000
INFO @ Thu, 22 Dec 2016 02:40:11: 17000000
INFO @ Thu, 22 Dec 2016 02:40:12: 18000000
INFO @ Thu, 22 Dec 2016 02:40:14: 19000000
INFO @ Thu, 22 Dec 2016 02:40:16: 20000000
INFO @ Thu, 22 Dec 2016 02:40:17: 21000000
INFO @ Thu, 22 Dec 2016 02:40:19: 22000000
INFO @ Thu, 22 Dec 2016 02:40:20: 23000000
INFO @ Thu, 22 Dec 2016 02:40:22: 24000000
INFO @ Thu, 22 Dec 2016 02:40:24: 25000000
INFO @ Thu, 22 Dec 2016 02:40:25: 26000000
INFO @ Thu, 22 Dec 2016 02:40:27: 27000000
INFO @ Thu, 22 Dec 2016 02:40:29: 28000000
INFO @ Thu, 22 Dec 2016 02:40:30: 29000000
INFO @ Thu, 22 Dec 2016 02:40:32: 30000000
INFO @ Thu, 22 Dec 2016 02:40:33: 31000000
INFO @ Thu, 22 Dec 2016 02:40:35: 32000000
INFO @ Thu, 22 Dec 2016 02:40:37: 33000000
INFO @ Thu, 22 Dec 2016 02:40:39: 34000000
INFO @ Thu, 22 Dec 2016 02:40:40: 35000000
INFO @ Thu, 22 Dec 2016 02:40:42: 36000000
INFO @ Thu, 22 Dec 2016 02:40:43: 37000000
INFO @ Thu, 22 Dec 2016 02:40:45: 38000000
INFO @ Thu, 22 Dec 2016 02:40:47: 39000000
INFO @ Thu, 22 Dec 2016 02:40:48: 40000000
INFO @ Thu, 22 Dec 2016 02:40:50: 41000000
INFO @ Thu, 22 Dec 2016 02:40:52: 42000000
INFO @ Thu, 22 Dec 2016 02:40:53: 43000000
INFO @ Thu, 22 Dec 2016 02:40:55: 44000000
INFO @ Thu, 22 Dec 2016 02:40:56: 45000000
INFO @ Thu, 22 Dec 2016 02:40:58: 46000000
INFO @ Thu, 22 Dec 2016 02:41:00: 47000000
INFO @ Thu, 22 Dec 2016 02:41:01: 48000000
INFO @ Thu, 22 Dec 2016 02:41:03: 49000000
INFO @ Thu, 22 Dec 2016 02:41:04: 50000000
INFO @ Thu, 22 Dec 2016 02:41:06: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 02:41:06: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 02:41:06: #1 total tags in treatment: 18040538
INFO @ Thu, 22 Dec 2016 02:41:06: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:41:06: #1 finished!
INFO @ Thu, 22 Dec 2016 02:41:06: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:41:06: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:41:06: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 02:41:06: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:41:06: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 02:41:06: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 02:46:54: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 02:46:54: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 02:46:54: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 02:46:54: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 02:46:54: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 02:53:31: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 02:53:31: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 02:53:32: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 02:53:32: Done!
INFO @ Thu, 22 Dec 2016 02:53:37:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/rep1/SRR1370912_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/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/rep1/SRR1370912_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 02:53:37: #1 read tag files...
INFO @ Thu, 22 Dec 2016 02:53:37: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 02:53:39: 1000000
INFO @ Thu, 22 Dec 2016 02:53:40: 2000000
INFO @ Thu, 22 Dec 2016 02:53:42: 3000000
INFO @ Thu, 22 Dec 2016 02:53:43: 4000000
INFO @ Thu, 22 Dec 2016 02:53:45: 5000000
INFO @ Thu, 22 Dec 2016 02:53:47: 6000000
INFO @ Thu, 22 Dec 2016 02:53:48: 7000000
INFO @ Thu, 22 Dec 2016 02:53:50: 8000000
INFO @ Thu, 22 Dec 2016 02:53:51: 9000000
INFO @ Thu, 22 Dec 2016 02:53:53: 10000000
INFO @ Thu, 22 Dec 2016 02:53:54: 11000000
INFO @ Thu, 22 Dec 2016 02:53:56: 12000000
INFO @ Thu, 22 Dec 2016 02:53:57: 13000000
INFO @ Thu, 22 Dec 2016 02:53:59: 14000000
INFO @ Thu, 22 Dec 2016 02:54:01: 15000000
INFO @ Thu, 22 Dec 2016 02:54:02: 16000000
INFO @ Thu, 22 Dec 2016 02:54:04: 17000000
INFO @ Thu, 22 Dec 2016 02:54:05: 18000000
INFO @ Thu, 22 Dec 2016 02:54:06: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 02:54:07: 1000000
INFO @ Thu, 22 Dec 2016 02:54:09: 2000000
INFO @ Thu, 22 Dec 2016 02:54:10: 3000000
INFO @ Thu, 22 Dec 2016 02:54:12: 4000000
INFO @ Thu, 22 Dec 2016 02:54:14: 5000000
INFO @ Thu, 22 Dec 2016 02:54:15: 6000000
INFO @ Thu, 22 Dec 2016 02:54:17: 7000000
INFO @ Thu, 22 Dec 2016 02:54:18: 8000000
INFO @ Thu, 22 Dec 2016 02:54:20: 9000000
INFO @ Thu, 22 Dec 2016 02:54:21: 10000000
INFO @ Thu, 22 Dec 2016 02:54:23: 11000000
INFO @ Thu, 22 Dec 2016 02:54:24: 12000000
INFO @ Thu, 22 Dec 2016 02:54:26: 13000000
INFO @ Thu, 22 Dec 2016 02:54:28: 14000000
INFO @ Thu, 22 Dec 2016 02:54:30: 15000000
INFO @ Thu, 22 Dec 2016 02:54:31: 16000000
INFO @ Thu, 22 Dec 2016 02:54:33: 17000000
INFO @ Thu, 22 Dec 2016 02:54:34: 18000000
INFO @ Thu, 22 Dec 2016 02:54:36: 19000000
INFO @ Thu, 22 Dec 2016 02:54:38: 20000000
INFO @ Thu, 22 Dec 2016 02:54:39: 21000000
INFO @ Thu, 22 Dec 2016 02:54:41: 22000000
INFO @ Thu, 22 Dec 2016 02:54:42: 23000000
INFO @ Thu, 22 Dec 2016 02:54:44: 24000000
INFO @ Thu, 22 Dec 2016 02:54:45: 25000000
INFO @ Thu, 22 Dec 2016 02:54:47: 26000000
INFO @ Thu, 22 Dec 2016 02:54:48: 27000000
INFO @ Thu, 22 Dec 2016 02:54:50: 28000000
INFO @ Thu, 22 Dec 2016 02:54:52: 29000000
INFO @ Thu, 22 Dec 2016 02:54:53: 30000000
INFO @ Thu, 22 Dec 2016 02:54:55: 31000000
INFO @ Thu, 22 Dec 2016 02:54:57: 32000000
INFO @ Thu, 22 Dec 2016 02:54:58: 33000000
INFO @ Thu, 22 Dec 2016 02:55:00: 34000000
INFO @ Thu, 22 Dec 2016 02:55:01: 35000000
INFO @ Thu, 22 Dec 2016 02:55:03: 36000000
INFO @ Thu, 22 Dec 2016 02:55:05: 37000000
INFO @ Thu, 22 Dec 2016 02:55:07: 38000000
INFO @ Thu, 22 Dec 2016 02:55:08: 39000000
INFO @ Thu, 22 Dec 2016 02:55:10: 40000000
INFO @ Thu, 22 Dec 2016 02:55:11: 41000000
INFO @ Thu, 22 Dec 2016 02:55:13: 42000000
INFO @ Thu, 22 Dec 2016 02:55:14: 43000000
INFO @ Thu, 22 Dec 2016 02:55:16: 44000000
INFO @ Thu, 22 Dec 2016 02:55:18: 45000000
INFO @ Thu, 22 Dec 2016 02:55:19: 46000000
INFO @ Thu, 22 Dec 2016 02:55:21: 47000000
INFO @ Thu, 22 Dec 2016 02:55:23: 48000000
INFO @ Thu, 22 Dec 2016 02:55:24: 49000000
INFO @ Thu, 22 Dec 2016 02:55:26: 50000000
INFO @ Thu, 22 Dec 2016 02:55:27: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 02:55:27: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 02:55:27: #1 total tags in treatment: 18040538
INFO @ Thu, 22 Dec 2016 02:55:27: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 02:55:27: #1 finished!
INFO @ Thu, 22 Dec 2016 02:55:27: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 02:55:27: #2 Skipped...
INFO @ Thu, 22 Dec 2016 02:55:27: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 02:55:27: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 02:55:27: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 02:55:27: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:03:19: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:07:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:07:49: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 03:07:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 03:07:56: Done!
INFO @ Thu, 22 Dec 2016 03:08:10: Read and build treatment bedGraph...
INFO @ Thu, 22 Dec 2016 03:08:48: Read and build control bedGraph...
INFO @ Thu, 22 Dec 2016 03:10:42: Build scoreTrackII...
INFO @ Thu, 22 Dec 2016 03:11:55: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 22 Dec 2016 03:18:34: Write bedGraph of scores...
INFO @ Thu, 22 Dec 2016 03:21:51: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/rep1/SRR1370912_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: 19492
exec_file: job_scripts/19492
submission_time: Wed Dec 21 14:14:54 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/ZNF653
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/chipseq.bds.20161221_141448_033/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/ZNF653/chipseq.bds.20161221_141448_033/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=51420.ZNF653.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/ZNF653,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=00:42:49, mem=4677.73690 GBs, io=50.65773, vmem=402.422M, maxvmem=3.953G
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 | 19496 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:57 | | End | 2016-12-22 03:57:37 | | Elapsed | 13:42:39 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_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--------------------
13459 (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 03:24:30:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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 03:24:30: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:24:30: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:24:32: 1000000
INFO @ Thu, 22 Dec 2016 03:24:34: 2000000
INFO @ Thu, 22 Dec 2016 03:24:35: 3000000
INFO @ Thu, 22 Dec 2016 03:24:37: 4000000
INFO @ Thu, 22 Dec 2016 03:24:39: 5000000
INFO @ Thu, 22 Dec 2016 03:24:41: 6000000
INFO @ Thu, 22 Dec 2016 03:24:43: 7000000
INFO @ Thu, 22 Dec 2016 03:24:45: 8000000
INFO @ Thu, 22 Dec 2016 03:24:47: 9000000
INFO @ Thu, 22 Dec 2016 03:24:47: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:24:49: 1000000
INFO @ Thu, 22 Dec 2016 03:24:51: 2000000
INFO @ Thu, 22 Dec 2016 03:24:52: 3000000
INFO @ Thu, 22 Dec 2016 03:24:54: 4000000
INFO @ Thu, 22 Dec 2016 03:24:56: 5000000
INFO @ Thu, 22 Dec 2016 03:24:58: 6000000
INFO @ Thu, 22 Dec 2016 03:24:59: 7000000
INFO @ Thu, 22 Dec 2016 03:25:01: 8000000
INFO @ Thu, 22 Dec 2016 03:25:03: 9000000
INFO @ Thu, 22 Dec 2016 03:25:04: 10000000
INFO @ Thu, 22 Dec 2016 03:25:06: 11000000
INFO @ Thu, 22 Dec 2016 03:25:08: 12000000
INFO @ Thu, 22 Dec 2016 03:25:10: 13000000
INFO @ Thu, 22 Dec 2016 03:25:11: 14000000
INFO @ Thu, 22 Dec 2016 03:25:13: 15000000
INFO @ Thu, 22 Dec 2016 03:25:15: 16000000
INFO @ Thu, 22 Dec 2016 03:25:17: 17000000
INFO @ Thu, 22 Dec 2016 03:25:18: 18000000
INFO @ Thu, 22 Dec 2016 03:25:20: 19000000
INFO @ Thu, 22 Dec 2016 03:25:22: 20000000
INFO @ Thu, 22 Dec 2016 03:25:24: 21000000
INFO @ Thu, 22 Dec 2016 03:25:26: 22000000
INFO @ Thu, 22 Dec 2016 03:25:27: 23000000
INFO @ Thu, 22 Dec 2016 03:25:29: 24000000
INFO @ Thu, 22 Dec 2016 03:25:31: 25000000
INFO @ Thu, 22 Dec 2016 03:25:32: 26000000
INFO @ Thu, 22 Dec 2016 03:25:34: 27000000
INFO @ Thu, 22 Dec 2016 03:25:36: 28000000
INFO @ Thu, 22 Dec 2016 03:25:38: 29000000
INFO @ Thu, 22 Dec 2016 03:25:39: 30000000
INFO @ Thu, 22 Dec 2016 03:25:41: 31000000
INFO @ Thu, 22 Dec 2016 03:25:43: 32000000
INFO @ Thu, 22 Dec 2016 03:25:44: 33000000
INFO @ Thu, 22 Dec 2016 03:25:46: 34000000
INFO @ Thu, 22 Dec 2016 03:25:48: 35000000
INFO @ Thu, 22 Dec 2016 03:25:49: 36000000
INFO @ Thu, 22 Dec 2016 03:25:51: 37000000
INFO @ Thu, 22 Dec 2016 03:25:53: 38000000
INFO @ Thu, 22 Dec 2016 03:25:55: 39000000
INFO @ Thu, 22 Dec 2016 03:25:56: 40000000
INFO @ Thu, 22 Dec 2016 03:25:58: 41000000
INFO @ Thu, 22 Dec 2016 03:26:00: 42000000
INFO @ Thu, 22 Dec 2016 03:26:01: 43000000
INFO @ Thu, 22 Dec 2016 03:26:03: 44000000
INFO @ Thu, 22 Dec 2016 03:26:05: 45000000
INFO @ Thu, 22 Dec 2016 03:26:06: 46000000
INFO @ Thu, 22 Dec 2016 03:26:08: 47000000
INFO @ Thu, 22 Dec 2016 03:26:10: 48000000
INFO @ Thu, 22 Dec 2016 03:26:12: 49000000
INFO @ Thu, 22 Dec 2016 03:26:13: 50000000
INFO @ Thu, 22 Dec 2016 03:26:15: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 03:26:15: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 03:26:15: #1 total tags in treatment: 9020269
INFO @ Thu, 22 Dec 2016 03:26:15: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:26:15: #1 finished!
INFO @ Thu, 22 Dec 2016 03:26:15: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:26:15: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:26:15: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 03:26:15: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:26:15: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 03:26:15: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:33:52: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 03:33:52: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 03:33:52: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 03:33:52: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 03:33:52: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:41:14: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:41:15: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 03:41:15: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 03:41:16: Done!
INFO @ Thu, 22 Dec 2016 03:41:19:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr1/SRR1370912_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 03:41:19: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:41:19: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:41:21: 1000000
INFO @ Thu, 22 Dec 2016 03:41:23: 2000000
INFO @ Thu, 22 Dec 2016 03:41:25: 3000000
INFO @ Thu, 22 Dec 2016 03:41:26: 4000000
INFO @ Thu, 22 Dec 2016 03:41:28: 5000000
INFO @ Thu, 22 Dec 2016 03:41:30: 6000000
INFO @ Thu, 22 Dec 2016 03:41:31: 7000000
INFO @ Thu, 22 Dec 2016 03:41:33: 8000000
INFO @ Thu, 22 Dec 2016 03:41:35: 9000000
INFO @ Thu, 22 Dec 2016 03:41:35: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:41:37: 1000000
INFO @ Thu, 22 Dec 2016 03:41:39: 2000000
INFO @ Thu, 22 Dec 2016 03:41:40: 3000000
INFO @ Thu, 22 Dec 2016 03:41:42: 4000000
INFO @ Thu, 22 Dec 2016 03:41:43: 5000000
INFO @ Thu, 22 Dec 2016 03:41:45: 6000000
INFO @ Thu, 22 Dec 2016 03:41:47: 7000000
INFO @ Thu, 22 Dec 2016 03:41:48: 8000000
INFO @ Thu, 22 Dec 2016 03:41:50: 9000000
INFO @ Thu, 22 Dec 2016 03:41:51: 10000000
INFO @ Thu, 22 Dec 2016 03:41:53: 11000000
INFO @ Thu, 22 Dec 2016 03:41:55: 12000000
INFO @ Thu, 22 Dec 2016 03:41:56: 13000000
INFO @ Thu, 22 Dec 2016 03:41:58: 14000000
INFO @ Thu, 22 Dec 2016 03:42:00: 15000000
INFO @ Thu, 22 Dec 2016 03:42:01: 16000000
INFO @ Thu, 22 Dec 2016 03:42:03: 17000000
INFO @ Thu, 22 Dec 2016 03:42:04: 18000000
INFO @ Thu, 22 Dec 2016 03:42:06: 19000000
INFO @ Thu, 22 Dec 2016 03:42:08: 20000000
INFO @ Thu, 22 Dec 2016 03:42:09: 21000000
INFO @ Thu, 22 Dec 2016 03:42:11: 22000000
INFO @ Thu, 22 Dec 2016 03:42:13: 23000000
INFO @ Thu, 22 Dec 2016 03:42:14: 24000000
INFO @ Thu, 22 Dec 2016 03:42:16: 25000000
INFO @ Thu, 22 Dec 2016 03:42:17: 26000000
INFO @ Thu, 22 Dec 2016 03:42:19: 27000000
INFO @ Thu, 22 Dec 2016 03:42:21: 28000000
INFO @ Thu, 22 Dec 2016 03:42:22: 29000000
INFO @ Thu, 22 Dec 2016 03:42:24: 30000000
INFO @ Thu, 22 Dec 2016 03:42:26: 31000000
INFO @ Thu, 22 Dec 2016 03:42:27: 32000000
INFO @ Thu, 22 Dec 2016 03:42:29: 33000000
INFO @ Thu, 22 Dec 2016 03:42:31: 34000000
INFO @ Thu, 22 Dec 2016 03:42:32: 35000000
INFO @ Thu, 22 Dec 2016 03:42:34: 36000000
INFO @ Thu, 22 Dec 2016 03:42:36: 37000000
INFO @ Thu, 22 Dec 2016 03:42:37: 38000000
INFO @ Thu, 22 Dec 2016 03:42:39: 39000000
INFO @ Thu, 22 Dec 2016 03:42:40: 40000000
INFO @ Thu, 22 Dec 2016 03:42:42: 41000000
INFO @ Thu, 22 Dec 2016 03:42:44: 42000000
INFO @ Thu, 22 Dec 2016 03:42:45: 43000000
INFO @ Thu, 22 Dec 2016 03:42:47: 44000000
INFO @ Thu, 22 Dec 2016 03:42:48: 45000000
INFO @ Thu, 22 Dec 2016 03:42:50: 46000000
INFO @ Thu, 22 Dec 2016 03:42:52: 47000000
INFO @ Thu, 22 Dec 2016 03:42:53: 48000000
INFO @ Thu, 22 Dec 2016 03:42:55: 49000000
INFO @ Thu, 22 Dec 2016 03:42:56: 50000000
INFO @ Thu, 22 Dec 2016 03:42:58: #1 tag size is determined as 51 bps
INFO @ Thu, 22 Dec 2016 03:42:58: #1 tag size = 51
INFO @ Thu, 22 Dec 2016 03:42:58: #1 total tags in treatment: 9020269
INFO @ Thu, 22 Dec 2016 03:42:58: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:42:58: #1 finished!
INFO @ Thu, 22 Dec 2016 03:42:58: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:42:58: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:42:58: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 03:42:58: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:42:58: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 03:42:58: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 03:50:35: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 03:57:06: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 03:57:11: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 03:57:16: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370912_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 03:57:20: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 19498 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:58 | | End | 2016-12-22 04:44:36 | | Elapsed | 14:29:37 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_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--------------------
62204 (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 03:45:19:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_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 03:45:19: #1 read tag files...
INFO @ Thu, 22 Dec 2016 03:45:19: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 03:45:27: 1000000
INFO @ Thu, 22 Dec 2016 03:45:35: 2000000
INFO @ Thu, 22 Dec 2016 03:45:42: 3000000
INFO @ Thu, 22 Dec 2016 03:45:50: 4000000
INFO @ Thu, 22 Dec 2016 03:45:58: 5000000
INFO @ Thu, 22 Dec 2016 03:46:06: 6000000
INFO @ Thu, 22 Dec 2016 03:46:14: 7000000
INFO @ Thu, 22 Dec 2016 03:46:22: 8000000
INFO @ Thu, 22 Dec 2016 03:46:30: 9000000
INFO @ Thu, 22 Dec 2016 03:46:31: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 03:46:39: 1000000
INFO @ Thu, 22 Dec 2016 03:46:47: 2000000
INFO @ Thu, 22 Dec 2016 03:46:54: 3000000
INFO @ Thu, 22 Dec 2016 03:47:02: 4000000
INFO @ Thu, 22 Dec 2016 03:47:10: 5000000
INFO @ Thu, 22 Dec 2016 03:47:18: 6000000
INFO @ Thu, 22 Dec 2016 03:47:25: 7000000
INFO @ Thu, 22 Dec 2016 03:47:33: 8000000
INFO @ Thu, 22 Dec 2016 03:47:41: 9000000
INFO @ Thu, 22 Dec 2016 03:47:49: 10000000
INFO @ Thu, 22 Dec 2016 03:47:57: 11000000
INFO @ Thu, 22 Dec 2016 03:48:05: 12000000
INFO @ Thu, 22 Dec 2016 03:48:13: 13000000
INFO @ Thu, 22 Dec 2016 03:48:20: 14000000
INFO @ Thu, 22 Dec 2016 03:48:28: 15000000
INFO @ Thu, 22 Dec 2016 03:48:36: 16000000
INFO @ Thu, 22 Dec 2016 03:48:44: 17000000
INFO @ Thu, 22 Dec 2016 03:48:52: 18000000
INFO @ Thu, 22 Dec 2016 03:48:59: 19000000
INFO @ Thu, 22 Dec 2016 03:49:07: 20000000
INFO @ Thu, 22 Dec 2016 03:49:15: 21000000
INFO @ Thu, 22 Dec 2016 03:49:22: 22000000
INFO @ Thu, 22 Dec 2016 03:49:30: 23000000
INFO @ Thu, 22 Dec 2016 03:49:38: 24000000
INFO @ Thu, 22 Dec 2016 03:49:46: 25000000
INFO @ Thu, 22 Dec 2016 03:49:53: 26000000
INFO @ Thu, 22 Dec 2016 03:50:01: 27000000
INFO @ Thu, 22 Dec 2016 03:50:09: 28000000
INFO @ Thu, 22 Dec 2016 03:50:17: 29000000
INFO @ Thu, 22 Dec 2016 03:50:24: 30000000
INFO @ Thu, 22 Dec 2016 03:50:32: 31000000
INFO @ Thu, 22 Dec 2016 03:50:40: 32000000
INFO @ Thu, 22 Dec 2016 03:50:48: 33000000
INFO @ Thu, 22 Dec 2016 03:50:55: 34000000
INFO @ Thu, 22 Dec 2016 03:51:03: 35000000
INFO @ Thu, 22 Dec 2016 03:51:10: 36000000
INFO @ Thu, 22 Dec 2016 03:51:18: 37000000
INFO @ Thu, 22 Dec 2016 03:51:26: 38000000
INFO @ Thu, 22 Dec 2016 03:51:33: 39000000
INFO @ Thu, 22 Dec 2016 03:51:41: 40000000
INFO @ Thu, 22 Dec 2016 03:51:49: 41000000
INFO @ Thu, 22 Dec 2016 03:51:56: 42000000
INFO @ Thu, 22 Dec 2016 03:52:04: 43000000
INFO @ Thu, 22 Dec 2016 03:52:12: 44000000
INFO @ Thu, 22 Dec 2016 03:52:20: 45000000
INFO @ Thu, 22 Dec 2016 03:52:27: 46000000
INFO @ Thu, 22 Dec 2016 03:52:36: 47000000
INFO @ Thu, 22 Dec 2016 03:52:44: 48000000
INFO @ Thu, 22 Dec 2016 03:52:51: 49000000
INFO @ Thu, 22 Dec 2016 03:52:59: 50000000
INFO @ Thu, 22 Dec 2016 03:53:04: #1 tag size is determined as 50 bps
INFO @ Thu, 22 Dec 2016 03:53:04: #1 tag size = 50
INFO @ Thu, 22 Dec 2016 03:53:04: #1 total tags in treatment: 9020269
INFO @ Thu, 22 Dec 2016 03:53:04: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 03:53:04: #1 finished!
INFO @ Thu, 22 Dec 2016 03:53:04: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 03:53:04: #2 Skipped...
INFO @ Thu, 22 Dec 2016 03:53:04: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 03:53:04: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 03:53:04: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 22 Dec 2016 03:53:04: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:01:25: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 22 Dec 2016 04:01:25: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Thu, 22 Dec 2016 04:01:25: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Thu, 22 Dec 2016 04:01:25: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 22 Dec 2016 04:01:25: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:18:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:18:55: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Thu, 22 Dec 2016 04:18:56: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Thu, 22 Dec 2016 04:18:57: Done!
INFO @ Thu, 22 Dec 2016 04:19:03:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_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/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/align/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Thu, 22 Dec 2016 04:19:03: #1 read tag files...
INFO @ Thu, 22 Dec 2016 04:19:03: #1 read treatment tags...
INFO @ Thu, 22 Dec 2016 04:19:11: 1000000
INFO @ Thu, 22 Dec 2016 04:19:18: 2000000
INFO @ Thu, 22 Dec 2016 04:19:26: 3000000
INFO @ Thu, 22 Dec 2016 04:19:34: 4000000
INFO @ Thu, 22 Dec 2016 04:19:42: 5000000
INFO @ Thu, 22 Dec 2016 04:19:50: 6000000
INFO @ Thu, 22 Dec 2016 04:19:58: 7000000
INFO @ Thu, 22 Dec 2016 04:20:06: 8000000
INFO @ Thu, 22 Dec 2016 04:20:14: 9000000
INFO @ Thu, 22 Dec 2016 04:20:15: #1.2 read input tags...
INFO @ Thu, 22 Dec 2016 04:20:23: 1000000
INFO @ Thu, 22 Dec 2016 04:20:30: 2000000
INFO @ Thu, 22 Dec 2016 04:20:38: 3000000
INFO @ Thu, 22 Dec 2016 04:20:46: 4000000
INFO @ Thu, 22 Dec 2016 04:20:53: 5000000
INFO @ Thu, 22 Dec 2016 04:21:01: 6000000
INFO @ Thu, 22 Dec 2016 04:21:09: 7000000
INFO @ Thu, 22 Dec 2016 04:21:17: 8000000
INFO @ Thu, 22 Dec 2016 04:21:24: 9000000
INFO @ Thu, 22 Dec 2016 04:21:32: 10000000
INFO @ Thu, 22 Dec 2016 04:21:40: 11000000
INFO @ Thu, 22 Dec 2016 04:21:48: 12000000
INFO @ Thu, 22 Dec 2016 04:21:55: 13000000
INFO @ Thu, 22 Dec 2016 04:22:03: 14000000
INFO @ Thu, 22 Dec 2016 04:22:11: 15000000
INFO @ Thu, 22 Dec 2016 04:22:18: 16000000
INFO @ Thu, 22 Dec 2016 04:22:26: 17000000
INFO @ Thu, 22 Dec 2016 04:22:34: 18000000
INFO @ Thu, 22 Dec 2016 04:22:42: 19000000
INFO @ Thu, 22 Dec 2016 04:22:49: 20000000
INFO @ Thu, 22 Dec 2016 04:22:57: 21000000
INFO @ Thu, 22 Dec 2016 04:23:05: 22000000
INFO @ Thu, 22 Dec 2016 04:23:13: 23000000
INFO @ Thu, 22 Dec 2016 04:23:20: 24000000
INFO @ Thu, 22 Dec 2016 04:23:28: 25000000
INFO @ Thu, 22 Dec 2016 04:23:36: 26000000
INFO @ Thu, 22 Dec 2016 04:23:44: 27000000
INFO @ Thu, 22 Dec 2016 04:23:51: 28000000
INFO @ Thu, 22 Dec 2016 04:23:59: 29000000
INFO @ Thu, 22 Dec 2016 04:24:07: 30000000
INFO @ Thu, 22 Dec 2016 04:24:15: 31000000
INFO @ Thu, 22 Dec 2016 04:24:22: 32000000
INFO @ Thu, 22 Dec 2016 04:24:30: 33000000
INFO @ Thu, 22 Dec 2016 04:24:38: 34000000
INFO @ Thu, 22 Dec 2016 04:24:45: 35000000
INFO @ Thu, 22 Dec 2016 04:24:53: 36000000
INFO @ Thu, 22 Dec 2016 04:25:01: 37000000
INFO @ Thu, 22 Dec 2016 04:25:08: 38000000
INFO @ Thu, 22 Dec 2016 04:25:16: 39000000
INFO @ Thu, 22 Dec 2016 04:25:24: 40000000
INFO @ Thu, 22 Dec 2016 04:25:31: 41000000
INFO @ Thu, 22 Dec 2016 04:25:39: 42000000
INFO @ Thu, 22 Dec 2016 04:25:47: 43000000
INFO @ Thu, 22 Dec 2016 04:25:55: 44000000
INFO @ Thu, 22 Dec 2016 04:26:02: 45000000
INFO @ Thu, 22 Dec 2016 04:26:10: 46000000
INFO @ Thu, 22 Dec 2016 04:26:18: 47000000
INFO @ Thu, 22 Dec 2016 04:26:25: 48000000
INFO @ Thu, 22 Dec 2016 04:26:33: 49000000
INFO @ Thu, 22 Dec 2016 04:26:41: 50000000
INFO @ Thu, 22 Dec 2016 04:26:45: #1 tag size is determined as 50 bps
INFO @ Thu, 22 Dec 2016 04:26:45: #1 tag size = 50
INFO @ Thu, 22 Dec 2016 04:26:45: #1 total tags in treatment: 9020269
INFO @ Thu, 22 Dec 2016 04:26:45: #1 total tags in control: 50000000
INFO @ Thu, 22 Dec 2016 04:26:45: #1 finished!
INFO @ Thu, 22 Dec 2016 04:26:45: #2 Build Peak Model...
INFO @ Thu, 22 Dec 2016 04:26:45: #2 Skipped...
INFO @ Thu, 22 Dec 2016 04:26:45: #2 Use 155 as fragment length
INFO @ Thu, 22 Dec 2016 04:26:45: #3 Call peaks...
INFO @ Thu, 22 Dec 2016 04:26:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Thu, 22 Dec 2016 04:26:45: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 22 Dec 2016 04:34:58: #3 Call peaks for each chromosome...
INFO @ Thu, 22 Dec 2016 04:43:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Thu, 22 Dec 2016 04:43:34: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Thu, 22 Dec 2016 04:43:51: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF653/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370912_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Thu, 22 Dec 2016 04:44:04: Done!
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