| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 19473 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-12-21 14:13:57 | | End | 2016-12-21 14:13:57 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/signal/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/signal/macs2/rep1/SRR1370890_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/KLF10/out/align/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/align/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1 -o "SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/signal/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/align/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1 -o "SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/signal/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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--------------------
7247 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Wed, 21 Dec 2016 20:33:14:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/rep1/SRR1370890_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Wed, 21 Dec 2016 20:33:14: #1 read tag files...
INFO @ Wed, 21 Dec 2016 20:33:14: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 20:33:16: 1000000
INFO @ Wed, 21 Dec 2016 20:33:18: 2000000
INFO @ Wed, 21 Dec 2016 20:33:20: 3000000
INFO @ Wed, 21 Dec 2016 20:33:22: 4000000
INFO @ Wed, 21 Dec 2016 20:33:23: 5000000
INFO @ Wed, 21 Dec 2016 20:33:25: 6000000
INFO @ Wed, 21 Dec 2016 20:33:27: 7000000
INFO @ Wed, 21 Dec 2016 20:33:29: 8000000
INFO @ Wed, 21 Dec 2016 20:33:30: 9000000
INFO @ Wed, 21 Dec 2016 20:33:32: 10000000
INFO @ Wed, 21 Dec 2016 20:33:34: 11000000
INFO @ Wed, 21 Dec 2016 20:33:36: 12000000
INFO @ Wed, 21 Dec 2016 20:33:37: 13000000
INFO @ Wed, 21 Dec 2016 20:33:39: 14000000
INFO @ Wed, 21 Dec 2016 20:33:41: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 20:33:42: 1000000
INFO @ Wed, 21 Dec 2016 20:33:44: 2000000
INFO @ Wed, 21 Dec 2016 20:33:46: 3000000
INFO @ Wed, 21 Dec 2016 20:33:48: 4000000
INFO @ Wed, 21 Dec 2016 20:33:50: 5000000
INFO @ Wed, 21 Dec 2016 20:33:51: 6000000
INFO @ Wed, 21 Dec 2016 20:33:53: 7000000
INFO @ Wed, 21 Dec 2016 20:33:55: 8000000
INFO @ Wed, 21 Dec 2016 20:33:56: 9000000
INFO @ Wed, 21 Dec 2016 20:33:58: 10000000
INFO @ Wed, 21 Dec 2016 20:34:00: 11000000
INFO @ Wed, 21 Dec 2016 20:34:02: 12000000
INFO @ Wed, 21 Dec 2016 20:34:03: 13000000
INFO @ Wed, 21 Dec 2016 20:34:05: 14000000
INFO @ Wed, 21 Dec 2016 20:34:07: 15000000
INFO @ Wed, 21 Dec 2016 20:34:09: 16000000
INFO @ Wed, 21 Dec 2016 20:34:10: 17000000
INFO @ Wed, 21 Dec 2016 20:34:12: 18000000
INFO @ Wed, 21 Dec 2016 20:34:14: 19000000
INFO @ Wed, 21 Dec 2016 20:34:16: 20000000
INFO @ Wed, 21 Dec 2016 20:34:17: 21000000
INFO @ Wed, 21 Dec 2016 20:34:19: 22000000
INFO @ Wed, 21 Dec 2016 20:34:21: 23000000
INFO @ Wed, 21 Dec 2016 20:34:23: 24000000
INFO @ Wed, 21 Dec 2016 20:34:24: 25000000
INFO @ Wed, 21 Dec 2016 20:34:26: 26000000
INFO @ Wed, 21 Dec 2016 20:34:28: 27000000
INFO @ Wed, 21 Dec 2016 20:34:30: 28000000
INFO @ Wed, 21 Dec 2016 20:34:31: 29000000
INFO @ Wed, 21 Dec 2016 20:34:33: 30000000
INFO @ Wed, 21 Dec 2016 20:34:35: 31000000
INFO @ Wed, 21 Dec 2016 20:34:37: 32000000
INFO @ Wed, 21 Dec 2016 20:34:38: 33000000
INFO @ Wed, 21 Dec 2016 20:34:40: 34000000
INFO @ Wed, 21 Dec 2016 20:34:42: 35000000
INFO @ Wed, 21 Dec 2016 20:34:44: 36000000
INFO @ Wed, 21 Dec 2016 20:34:45: 37000000
INFO @ Wed, 21 Dec 2016 20:34:47: 38000000
INFO @ Wed, 21 Dec 2016 20:34:49: 39000000
INFO @ Wed, 21 Dec 2016 20:34:51: 40000000
INFO @ Wed, 21 Dec 2016 20:34:52: 41000000
INFO @ Wed, 21 Dec 2016 20:34:54: 42000000
INFO @ Wed, 21 Dec 2016 20:34:56: 43000000
INFO @ Wed, 21 Dec 2016 20:34:57: 44000000
INFO @ Wed, 21 Dec 2016 20:34:59: 45000000
INFO @ Wed, 21 Dec 2016 20:35:01: 46000000
INFO @ Wed, 21 Dec 2016 20:35:03: 47000000
INFO @ Wed, 21 Dec 2016 20:35:04: 48000000
INFO @ Wed, 21 Dec 2016 20:35:06: 49000000
INFO @ Wed, 21 Dec 2016 20:35:08: 50000000
INFO @ Wed, 21 Dec 2016 20:35:10: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 20:35:10: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 20:35:10: #1 total tags in treatment: 14875166
INFO @ Wed, 21 Dec 2016 20:35:10: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 20:35:10: #1 finished!
INFO @ Wed, 21 Dec 2016 20:35:10: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 20:35:10: #2 Skipped...
INFO @ Wed, 21 Dec 2016 20:35:10: #2 Use 155 as fragment length
INFO @ Wed, 21 Dec 2016 20:35:10: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 20:35:10: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Wed, 21 Dec 2016 20:35:10: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 20:39:38: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Wed, 21 Dec 2016 20:39:38: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Wed, 21 Dec 2016 20:39:38: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Wed, 21 Dec 2016 20:39:38: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Wed, 21 Dec 2016 20:39:38: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 20:45:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 20:45:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Wed, 21 Dec 2016 20:45:37: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Wed, 21 Dec 2016 20:45:37: Done!
INFO @ Wed, 21 Dec 2016 20:45:40:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_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/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/rep1/SRR1370890_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Wed, 21 Dec 2016 20:45:40: #1 read tag files...
INFO @ Wed, 21 Dec 2016 20:45:40: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 20:45:42: 1000000
INFO @ Wed, 21 Dec 2016 20:45:44: 2000000
INFO @ Wed, 21 Dec 2016 20:45:45: 3000000
INFO @ Wed, 21 Dec 2016 20:45:47: 4000000
INFO @ Wed, 21 Dec 2016 20:45:49: 5000000
INFO @ Wed, 21 Dec 2016 20:45:51: 6000000
INFO @ Wed, 21 Dec 2016 20:45:52: 7000000
INFO @ Wed, 21 Dec 2016 20:45:54: 8000000
INFO @ Wed, 21 Dec 2016 20:45:56: 9000000
INFO @ Wed, 21 Dec 2016 20:45:57: 10000000
INFO @ Wed, 21 Dec 2016 20:45:59: 11000000
INFO @ Wed, 21 Dec 2016 20:46:01: 12000000
INFO @ Wed, 21 Dec 2016 20:46:02: 13000000
INFO @ Wed, 21 Dec 2016 20:46:04: 14000000
INFO @ Wed, 21 Dec 2016 20:46:06: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 20:46:08: 1000000
INFO @ Wed, 21 Dec 2016 20:46:09: 2000000
INFO @ Wed, 21 Dec 2016 20:46:11: 3000000
INFO @ Wed, 21 Dec 2016 20:46:13: 4000000
INFO @ Wed, 21 Dec 2016 20:46:15: 5000000
INFO @ Wed, 21 Dec 2016 20:46:16: 6000000
INFO @ Wed, 21 Dec 2016 20:46:18: 7000000
INFO @ Wed, 21 Dec 2016 20:46:20: 8000000
INFO @ Wed, 21 Dec 2016 20:46:22: 9000000
INFO @ Wed, 21 Dec 2016 20:46:23: 10000000
INFO @ Wed, 21 Dec 2016 20:46:25: 11000000
INFO @ Wed, 21 Dec 2016 20:46:27: 12000000
INFO @ Wed, 21 Dec 2016 20:46:29: 13000000
INFO @ Wed, 21 Dec 2016 20:46:30: 14000000
INFO @ Wed, 21 Dec 2016 20:46:32: 15000000
INFO @ Wed, 21 Dec 2016 20:46:34: 16000000
INFO @ Wed, 21 Dec 2016 20:46:36: 17000000
INFO @ Wed, 21 Dec 2016 20:46:37: 18000000
INFO @ Wed, 21 Dec 2016 20:46:39: 19000000
INFO @ Wed, 21 Dec 2016 20:46:41: 20000000
INFO @ Wed, 21 Dec 2016 20:46:43: 21000000
INFO @ Wed, 21 Dec 2016 20:46:44: 22000000
INFO @ Wed, 21 Dec 2016 20:46:46: 23000000
INFO @ Wed, 21 Dec 2016 20:46:48: 24000000
INFO @ Wed, 21 Dec 2016 20:46:49: 25000000
INFO @ Wed, 21 Dec 2016 20:46:51: 26000000
INFO @ Wed, 21 Dec 2016 20:46:53: 27000000
INFO @ Wed, 21 Dec 2016 20:46:55: 28000000
INFO @ Wed, 21 Dec 2016 20:46:56: 29000000
INFO @ Wed, 21 Dec 2016 20:46:58: 30000000
INFO @ Wed, 21 Dec 2016 20:47:00: 31000000
INFO @ Wed, 21 Dec 2016 20:47:02: 32000000
INFO @ Wed, 21 Dec 2016 20:47:03: 33000000
INFO @ Wed, 21 Dec 2016 20:47:05: 34000000
INFO @ Wed, 21 Dec 2016 20:47:07: 35000000
INFO @ Wed, 21 Dec 2016 20:47:09: 36000000
INFO @ Wed, 21 Dec 2016 20:47:10: 37000000
INFO @ Wed, 21 Dec 2016 20:47:12: 38000000
INFO @ Wed, 21 Dec 2016 20:47:14: 39000000
INFO @ Wed, 21 Dec 2016 20:47:16: 40000000
INFO @ Wed, 21 Dec 2016 20:47:17: 41000000
INFO @ Wed, 21 Dec 2016 20:47:19: 42000000
INFO @ Wed, 21 Dec 2016 20:47:21: 43000000
INFO @ Wed, 21 Dec 2016 20:47:23: 44000000
INFO @ Wed, 21 Dec 2016 20:47:24: 45000000
INFO @ Wed, 21 Dec 2016 20:47:26: 46000000
INFO @ Wed, 21 Dec 2016 20:47:28: 47000000
INFO @ Wed, 21 Dec 2016 20:47:30: 48000000
INFO @ Wed, 21 Dec 2016 20:47:31: 49000000
INFO @ Wed, 21 Dec 2016 20:47:33: 50000000
INFO @ Wed, 21 Dec 2016 20:47:35: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 20:47:35: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 20:47:35: #1 total tags in treatment: 14875166
INFO @ Wed, 21 Dec 2016 20:47:35: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 20:47:35: #1 finished!
INFO @ Wed, 21 Dec 2016 20:47:35: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 20:47:35: #2 Skipped...
INFO @ Wed, 21 Dec 2016 20:47:35: #2 Use 155 as fragment length
INFO @ Wed, 21 Dec 2016 20:47:35: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 20:47:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Wed, 21 Dec 2016 20:47:35: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 20:51:30: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 20:54:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 20:54:57: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Wed, 21 Dec 2016 20:55:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Wed, 21 Dec 2016 20:55:05: Done!
INFO @ Wed, 21 Dec 2016 20:55:22: Read and build treatment bedGraph...
INFO @ Wed, 21 Dec 2016 20:55:53: Read and build control bedGraph...
INFO @ Wed, 21 Dec 2016 20:57:44: Build scoreTrackII...
INFO @ Wed, 21 Dec 2016 20:58:34: Calculate scores comparing treatment and control by 'FE'...
INFO @ Wed, 21 Dec 2016 21:03:35: Write bedGraph of scores...
INFO @ Wed, 21 Dec 2016 21:06:28: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/rep1/SRR1370890_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: 19473
exec_file: job_scripts/19473
submission_time: Wed Dec 21 14:13:57 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /software/samtools/samtools-1.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/chipseq.bds.20161221_141348_097/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/KLF10/chipseq.bds.20161221_141348_097/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=46200.KLF10.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/KLF10,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=00:33:30, mem=3518.89441 GBs, io=49.67893, vmem=262.902M, maxvmem=4.025G
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@kadru" dropped because it is full
queue instance "q@nandi" 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 | 19475 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:13:59 | | End | 2016-12-21 21:57:57 | | Elapsed | 07:43:58 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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--------------------
8007 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Wed, 21 Dec 2016 21:37:59:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Wed, 21 Dec 2016 21:37:59: #1 read tag files...
INFO @ Wed, 21 Dec 2016 21:37:59: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 21:38:01: 1000000
INFO @ Wed, 21 Dec 2016 21:38:03: 2000000
INFO @ Wed, 21 Dec 2016 21:38:05: 3000000
INFO @ Wed, 21 Dec 2016 21:38:07: 4000000
INFO @ Wed, 21 Dec 2016 21:38:08: 5000000
INFO @ Wed, 21 Dec 2016 21:38:10: 6000000
INFO @ Wed, 21 Dec 2016 21:38:12: 7000000
INFO @ Wed, 21 Dec 2016 21:38:13: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 21:38:15: 1000000
INFO @ Wed, 21 Dec 2016 21:38:17: 2000000
INFO @ Wed, 21 Dec 2016 21:38:19: 3000000
INFO @ Wed, 21 Dec 2016 21:38:20: 4000000
INFO @ Wed, 21 Dec 2016 21:38:22: 5000000
INFO @ Wed, 21 Dec 2016 21:38:24: 6000000
INFO @ Wed, 21 Dec 2016 21:38:25: 7000000
INFO @ Wed, 21 Dec 2016 21:38:27: 8000000
INFO @ Wed, 21 Dec 2016 21:38:29: 9000000
INFO @ Wed, 21 Dec 2016 21:38:31: 10000000
INFO @ Wed, 21 Dec 2016 21:38:32: 11000000
INFO @ Wed, 21 Dec 2016 21:38:34: 12000000
INFO @ Wed, 21 Dec 2016 21:38:36: 13000000
INFO @ Wed, 21 Dec 2016 21:38:37: 14000000
INFO @ Wed, 21 Dec 2016 21:38:39: 15000000
INFO @ Wed, 21 Dec 2016 21:38:41: 16000000
INFO @ Wed, 21 Dec 2016 21:38:43: 17000000
INFO @ Wed, 21 Dec 2016 21:38:44: 18000000
INFO @ Wed, 21 Dec 2016 21:38:46: 19000000
INFO @ Wed, 21 Dec 2016 21:38:48: 20000000
INFO @ Wed, 21 Dec 2016 21:38:50: 21000000
INFO @ Wed, 21 Dec 2016 21:38:51: 22000000
INFO @ Wed, 21 Dec 2016 21:38:53: 23000000
INFO @ Wed, 21 Dec 2016 21:38:55: 24000000
INFO @ Wed, 21 Dec 2016 21:38:56: 25000000
INFO @ Wed, 21 Dec 2016 21:38:58: 26000000
INFO @ Wed, 21 Dec 2016 21:39:00: 27000000
INFO @ Wed, 21 Dec 2016 21:39:02: 28000000
INFO @ Wed, 21 Dec 2016 21:39:03: 29000000
INFO @ Wed, 21 Dec 2016 21:39:05: 30000000
INFO @ Wed, 21 Dec 2016 21:39:07: 31000000
INFO @ Wed, 21 Dec 2016 21:39:09: 32000000
INFO @ Wed, 21 Dec 2016 21:39:10: 33000000
INFO @ Wed, 21 Dec 2016 21:39:12: 34000000
INFO @ Wed, 21 Dec 2016 21:39:14: 35000000
INFO @ Wed, 21 Dec 2016 21:39:15: 36000000
INFO @ Wed, 21 Dec 2016 21:39:17: 37000000
INFO @ Wed, 21 Dec 2016 21:39:19: 38000000
INFO @ Wed, 21 Dec 2016 21:39:21: 39000000
INFO @ Wed, 21 Dec 2016 21:39:22: 40000000
INFO @ Wed, 21 Dec 2016 21:39:24: 41000000
INFO @ Wed, 21 Dec 2016 21:39:26: 42000000
INFO @ Wed, 21 Dec 2016 21:39:28: 43000000
INFO @ Wed, 21 Dec 2016 21:39:29: 44000000
INFO @ Wed, 21 Dec 2016 21:39:31: 45000000
INFO @ Wed, 21 Dec 2016 21:39:33: 46000000
INFO @ Wed, 21 Dec 2016 21:39:34: 47000000
INFO @ Wed, 21 Dec 2016 21:39:36: 48000000
INFO @ Wed, 21 Dec 2016 21:39:38: 49000000
INFO @ Wed, 21 Dec 2016 21:39:40: 50000000
INFO @ Wed, 21 Dec 2016 21:39:41: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 21:39:41: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 21:39:41: #1 total tags in treatment: 7437583
INFO @ Wed, 21 Dec 2016 21:39:41: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 21:39:41: #1 finished!
INFO @ Wed, 21 Dec 2016 21:39:41: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 21:39:41: #2 Skipped...
INFO @ Wed, 21 Dec 2016 21:39:41: #2 Use 155 as fragment length
INFO @ Wed, 21 Dec 2016 21:39:41: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 21:39:41: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Wed, 21 Dec 2016 21:39:41: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 21:43:17: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Wed, 21 Dec 2016 21:43:17: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Wed, 21 Dec 2016 21:43:17: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Wed, 21 Dec 2016 21:43:17: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Wed, 21 Dec 2016 21:43:17: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 21:48:24: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 21:48:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Wed, 21 Dec 2016 21:48:26: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Wed, 21 Dec 2016 21:48:27: Done!
INFO @ Wed, 21 Dec 2016 21:48:30:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Wed, 21 Dec 2016 21:48:30: #1 read tag files...
INFO @ Wed, 21 Dec 2016 21:48:30: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 21:48:32: 1000000
INFO @ Wed, 21 Dec 2016 21:48:34: 2000000
INFO @ Wed, 21 Dec 2016 21:48:35: 3000000
INFO @ Wed, 21 Dec 2016 21:48:37: 4000000
INFO @ Wed, 21 Dec 2016 21:48:39: 5000000
INFO @ Wed, 21 Dec 2016 21:48:40: 6000000
INFO @ Wed, 21 Dec 2016 21:48:42: 7000000
INFO @ Wed, 21 Dec 2016 21:48:43: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 21:48:45: 1000000
INFO @ Wed, 21 Dec 2016 21:48:46: 2000000
INFO @ Wed, 21 Dec 2016 21:48:48: 3000000
INFO @ Wed, 21 Dec 2016 21:48:50: 4000000
INFO @ Wed, 21 Dec 2016 21:48:51: 5000000
INFO @ Wed, 21 Dec 2016 21:48:53: 6000000
INFO @ Wed, 21 Dec 2016 21:48:54: 7000000
INFO @ Wed, 21 Dec 2016 21:48:56: 8000000
INFO @ Wed, 21 Dec 2016 21:48:57: 9000000
INFO @ Wed, 21 Dec 2016 21:48:59: 10000000
INFO @ Wed, 21 Dec 2016 21:49:01: 11000000
INFO @ Wed, 21 Dec 2016 21:49:02: 12000000
INFO @ Wed, 21 Dec 2016 21:49:04: 13000000
INFO @ Wed, 21 Dec 2016 21:49:05: 14000000
INFO @ Wed, 21 Dec 2016 21:49:07: 15000000
INFO @ Wed, 21 Dec 2016 21:49:09: 16000000
INFO @ Wed, 21 Dec 2016 21:49:10: 17000000
INFO @ Wed, 21 Dec 2016 21:49:12: 18000000
INFO @ Wed, 21 Dec 2016 21:49:14: 19000000
INFO @ Wed, 21 Dec 2016 21:49:15: 20000000
INFO @ Wed, 21 Dec 2016 21:49:17: 21000000
INFO @ Wed, 21 Dec 2016 21:49:18: 22000000
INFO @ Wed, 21 Dec 2016 21:49:20: 23000000
INFO @ Wed, 21 Dec 2016 21:49:21: 24000000
INFO @ Wed, 21 Dec 2016 21:49:23: 25000000
INFO @ Wed, 21 Dec 2016 21:49:24: 26000000
INFO @ Wed, 21 Dec 2016 21:49:26: 27000000
INFO @ Wed, 21 Dec 2016 21:49:28: 28000000
INFO @ Wed, 21 Dec 2016 21:49:29: 29000000
INFO @ Wed, 21 Dec 2016 21:49:31: 30000000
INFO @ Wed, 21 Dec 2016 21:49:32: 31000000
INFO @ Wed, 21 Dec 2016 21:49:34: 32000000
INFO @ Wed, 21 Dec 2016 21:49:35: 33000000
INFO @ Wed, 21 Dec 2016 21:49:37: 34000000
INFO @ Wed, 21 Dec 2016 21:49:39: 35000000
INFO @ Wed, 21 Dec 2016 21:49:40: 36000000
INFO @ Wed, 21 Dec 2016 21:49:42: 37000000
INFO @ Wed, 21 Dec 2016 21:49:43: 38000000
INFO @ Wed, 21 Dec 2016 21:49:45: 39000000
INFO @ Wed, 21 Dec 2016 21:49:46: 40000000
INFO @ Wed, 21 Dec 2016 21:49:48: 41000000
INFO @ Wed, 21 Dec 2016 21:49:49: 42000000
INFO @ Wed, 21 Dec 2016 21:49:51: 43000000
INFO @ Wed, 21 Dec 2016 21:49:53: 44000000
INFO @ Wed, 21 Dec 2016 21:49:54: 45000000
INFO @ Wed, 21 Dec 2016 21:49:56: 46000000
INFO @ Wed, 21 Dec 2016 21:49:57: 47000000
INFO @ Wed, 21 Dec 2016 21:49:59: 48000000
INFO @ Wed, 21 Dec 2016 21:50:00: 49000000
INFO @ Wed, 21 Dec 2016 21:50:02: 50000000
INFO @ Wed, 21 Dec 2016 21:50:04: #1 tag size is determined as 68 bps
INFO @ Wed, 21 Dec 2016 21:50:04: #1 tag size = 68
INFO @ Wed, 21 Dec 2016 21:50:04: #1 total tags in treatment: 7437583
INFO @ Wed, 21 Dec 2016 21:50:04: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 21:50:04: #1 finished!
INFO @ Wed, 21 Dec 2016 21:50:04: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 21:50:04: #2 Skipped...
INFO @ Wed, 21 Dec 2016 21:50:04: #2 Use 155 as fragment length
INFO @ Wed, 21 Dec 2016 21:50:04: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 21:50:04: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Wed, 21 Dec 2016 21:50:04: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 21:53:40: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 21:57:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 21:57:29: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Wed, 21 Dec 2016 21:57:33: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370890_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Wed, 21 Dec 2016 21:57:38: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 19478 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-12-21 14:14:01 | | End | 2016-12-21 23:01:19 | | Elapsed | 08:47:18 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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--------------------
8786 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO @ Wed, 21 Dec 2016 22:40:59:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Wed, 21 Dec 2016 22:40:59: #1 read tag files...
INFO @ Wed, 21 Dec 2016 22:40:59: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 22:41:02: 1000000
INFO @ Wed, 21 Dec 2016 22:41:03: 2000000
INFO @ Wed, 21 Dec 2016 22:41:05: 3000000
INFO @ Wed, 21 Dec 2016 22:41:07: 4000000
INFO @ Wed, 21 Dec 2016 22:41:09: 5000000
INFO @ Wed, 21 Dec 2016 22:41:11: 6000000
INFO @ Wed, 21 Dec 2016 22:41:12: 7000000
INFO @ Wed, 21 Dec 2016 22:41:14: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 22:41:15: 1000000
INFO @ Wed, 21 Dec 2016 22:41:17: 2000000
INFO @ Wed, 21 Dec 2016 22:41:19: 3000000
INFO @ Wed, 21 Dec 2016 22:41:21: 4000000
INFO @ Wed, 21 Dec 2016 22:41:22: 5000000
INFO @ Wed, 21 Dec 2016 22:41:24: 6000000
INFO @ Wed, 21 Dec 2016 22:41:26: 7000000
INFO @ Wed, 21 Dec 2016 22:41:27: 8000000
INFO @ Wed, 21 Dec 2016 22:41:29: 9000000
INFO @ Wed, 21 Dec 2016 22:41:31: 10000000
INFO @ Wed, 21 Dec 2016 22:41:32: 11000000
INFO @ Wed, 21 Dec 2016 22:41:34: 12000000
INFO @ Wed, 21 Dec 2016 22:41:36: 13000000
INFO @ Wed, 21 Dec 2016 22:41:37: 14000000
INFO @ Wed, 21 Dec 2016 22:41:39: 15000000
INFO @ Wed, 21 Dec 2016 22:41:41: 16000000
INFO @ Wed, 21 Dec 2016 22:41:42: 17000000
INFO @ Wed, 21 Dec 2016 22:41:44: 18000000
INFO @ Wed, 21 Dec 2016 22:41:46: 19000000
INFO @ Wed, 21 Dec 2016 22:41:47: 20000000
INFO @ Wed, 21 Dec 2016 22:41:49: 21000000
INFO @ Wed, 21 Dec 2016 22:41:51: 22000000
INFO @ Wed, 21 Dec 2016 22:41:53: 23000000
INFO @ Wed, 21 Dec 2016 22:41:54: 24000000
INFO @ Wed, 21 Dec 2016 22:41:56: 25000000
INFO @ Wed, 21 Dec 2016 22:41:57: 26000000
INFO @ Wed, 21 Dec 2016 22:41:59: 27000000
INFO @ Wed, 21 Dec 2016 22:42:01: 28000000
INFO @ Wed, 21 Dec 2016 22:42:03: 29000000
INFO @ Wed, 21 Dec 2016 22:42:04: 30000000
INFO @ Wed, 21 Dec 2016 22:42:06: 31000000
INFO @ Wed, 21 Dec 2016 22:42:08: 32000000
INFO @ Wed, 21 Dec 2016 22:42:09: 33000000
INFO @ Wed, 21 Dec 2016 22:42:11: 34000000
INFO @ Wed, 21 Dec 2016 22:42:13: 35000000
INFO @ Wed, 21 Dec 2016 22:42:14: 36000000
INFO @ Wed, 21 Dec 2016 22:42:16: 37000000
INFO @ Wed, 21 Dec 2016 22:42:18: 38000000
INFO @ Wed, 21 Dec 2016 22:42:19: 39000000
INFO @ Wed, 21 Dec 2016 22:42:21: 40000000
INFO @ Wed, 21 Dec 2016 22:42:23: 41000000
INFO @ Wed, 21 Dec 2016 22:42:24: 42000000
INFO @ Wed, 21 Dec 2016 22:42:26: 43000000
INFO @ Wed, 21 Dec 2016 22:42:28: 44000000
INFO @ Wed, 21 Dec 2016 22:42:29: 45000000
INFO @ Wed, 21 Dec 2016 22:42:31: 46000000
INFO @ Wed, 21 Dec 2016 22:42:33: 47000000
INFO @ Wed, 21 Dec 2016 22:42:34: 48000000
INFO @ Wed, 21 Dec 2016 22:42:36: 49000000
INFO @ Wed, 21 Dec 2016 22:42:38: 50000000
INFO @ Wed, 21 Dec 2016 22:42:39: #1 tag size is determined as 69 bps
INFO @ Wed, 21 Dec 2016 22:42:39: #1 tag size = 69
INFO @ Wed, 21 Dec 2016 22:42:39: #1 total tags in treatment: 7437583
INFO @ Wed, 21 Dec 2016 22:42:39: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 22:42:39: #1 finished!
INFO @ Wed, 21 Dec 2016 22:42:39: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 22:42:39: #2 Skipped...
INFO @ Wed, 21 Dec 2016 22:42:39: #2 Use 155 as fragment length
INFO @ Wed, 21 Dec 2016 22:42:39: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 22:42:39: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Wed, 21 Dec 2016 22:42:39: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 22:46:14: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Wed, 21 Dec 2016 22:46:14: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Wed, 21 Dec 2016 22:46:14: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Wed, 21 Dec 2016 22:46:14: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Wed, 21 Dec 2016 22:46:14: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 22:51:35: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 22:51:36: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Wed, 21 Dec 2016 22:51:37: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Wed, 21 Dec 2016 22:51:37: Done!
INFO @ Wed, 21 Dec 2016 22:51:40:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_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/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/align/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Wed, 21 Dec 2016 22:51:40: #1 read tag files...
INFO @ Wed, 21 Dec 2016 22:51:40: #1 read treatment tags...
INFO @ Wed, 21 Dec 2016 22:51:42: 1000000
INFO @ Wed, 21 Dec 2016 22:51:44: 2000000
INFO @ Wed, 21 Dec 2016 22:51:46: 3000000
INFO @ Wed, 21 Dec 2016 22:51:48: 4000000
INFO @ Wed, 21 Dec 2016 22:51:50: 5000000
INFO @ Wed, 21 Dec 2016 22:51:52: 6000000
INFO @ Wed, 21 Dec 2016 22:51:53: 7000000
INFO @ Wed, 21 Dec 2016 22:51:55: #1.2 read input tags...
INFO @ Wed, 21 Dec 2016 22:51:57: 1000000
INFO @ Wed, 21 Dec 2016 22:51:58: 2000000
INFO @ Wed, 21 Dec 2016 22:52:00: 3000000
INFO @ Wed, 21 Dec 2016 22:52:02: 4000000
INFO @ Wed, 21 Dec 2016 22:52:04: 5000000
INFO @ Wed, 21 Dec 2016 22:52:05: 6000000
INFO @ Wed, 21 Dec 2016 22:52:07: 7000000
INFO @ Wed, 21 Dec 2016 22:52:09: 8000000
INFO @ Wed, 21 Dec 2016 22:52:11: 9000000
INFO @ Wed, 21 Dec 2016 22:52:12: 10000000
INFO @ Wed, 21 Dec 2016 22:52:14: 11000000
INFO @ Wed, 21 Dec 2016 22:52:16: 12000000
INFO @ Wed, 21 Dec 2016 22:52:18: 13000000
INFO @ Wed, 21 Dec 2016 22:52:19: 14000000
INFO @ Wed, 21 Dec 2016 22:52:21: 15000000
INFO @ Wed, 21 Dec 2016 22:52:23: 16000000
INFO @ Wed, 21 Dec 2016 22:52:25: 17000000
INFO @ Wed, 21 Dec 2016 22:52:27: 18000000
INFO @ Wed, 21 Dec 2016 22:52:28: 19000000
INFO @ Wed, 21 Dec 2016 22:52:30: 20000000
INFO @ Wed, 21 Dec 2016 22:52:32: 21000000
INFO @ Wed, 21 Dec 2016 22:52:34: 22000000
INFO @ Wed, 21 Dec 2016 22:52:35: 23000000
INFO @ Wed, 21 Dec 2016 22:52:37: 24000000
INFO @ Wed, 21 Dec 2016 22:52:39: 25000000
INFO @ Wed, 21 Dec 2016 22:52:41: 26000000
INFO @ Wed, 21 Dec 2016 22:52:42: 27000000
INFO @ Wed, 21 Dec 2016 22:52:44: 28000000
INFO @ Wed, 21 Dec 2016 22:52:46: 29000000
INFO @ Wed, 21 Dec 2016 22:52:48: 30000000
INFO @ Wed, 21 Dec 2016 22:52:49: 31000000
INFO @ Wed, 21 Dec 2016 22:52:51: 32000000
INFO @ Wed, 21 Dec 2016 22:52:53: 33000000
INFO @ Wed, 21 Dec 2016 22:52:55: 34000000
INFO @ Wed, 21 Dec 2016 22:52:56: 35000000
INFO @ Wed, 21 Dec 2016 22:52:58: 36000000
INFO @ Wed, 21 Dec 2016 22:53:00: 37000000
INFO @ Wed, 21 Dec 2016 22:53:01: 38000000
INFO @ Wed, 21 Dec 2016 22:53:03: 39000000
INFO @ Wed, 21 Dec 2016 22:53:05: 40000000
INFO @ Wed, 21 Dec 2016 22:53:07: 41000000
INFO @ Wed, 21 Dec 2016 22:53:08: 42000000
INFO @ Wed, 21 Dec 2016 22:53:10: 43000000
INFO @ Wed, 21 Dec 2016 22:53:12: 44000000
INFO @ Wed, 21 Dec 2016 22:53:14: 45000000
INFO @ Wed, 21 Dec 2016 22:53:15: 46000000
INFO @ Wed, 21 Dec 2016 22:53:17: 47000000
INFO @ Wed, 21 Dec 2016 22:53:19: 48000000
INFO @ Wed, 21 Dec 2016 22:53:21: 49000000
INFO @ Wed, 21 Dec 2016 22:53:22: 50000000
INFO @ Wed, 21 Dec 2016 22:53:24: #1 tag size is determined as 69 bps
INFO @ Wed, 21 Dec 2016 22:53:24: #1 tag size = 69
INFO @ Wed, 21 Dec 2016 22:53:24: #1 total tags in treatment: 7437583
INFO @ Wed, 21 Dec 2016 22:53:24: #1 total tags in control: 50000000
INFO @ Wed, 21 Dec 2016 22:53:24: #1 finished!
INFO @ Wed, 21 Dec 2016 22:53:24: #2 Build Peak Model...
INFO @ Wed, 21 Dec 2016 22:53:24: #2 Skipped...
INFO @ Wed, 21 Dec 2016 22:53:24: #2 Use 155 as fragment length
INFO @ Wed, 21 Dec 2016 22:53:24: #3 Call peaks...
INFO @ Wed, 21 Dec 2016 22:53:24: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Wed, 21 Dec 2016 22:53:24: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 21 Dec 2016 22:57:00: #3 Call peaks for each chromosome...
INFO @ Wed, 21 Dec 2016 23:00:45: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Wed, 21 Dec 2016 23:00:51: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Wed, 21 Dec 2016 23:00:56: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF10/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370890_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Wed, 21 Dec 2016 23:01:00: Done!
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