| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 4357 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-11-06 18:09:26 | | End | 2016-11-06 18:09:26 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/signal/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/signal/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
| | Dependencies | | |
# SYS command. line 69
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 88
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz
# SYS command. line 92
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 100
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1 -o "ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/signal/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1 -o "ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/signal/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
43124 (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 @ Sun, 06 Nov 2016 18:17:45:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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 @ Sun, 06 Nov 2016 18:17:45: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:17:45: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:17:47: 1000000
INFO @ Sun, 06 Nov 2016 18:17:48: 2000000
INFO @ Sun, 06 Nov 2016 18:17:50: 3000000
INFO @ Sun, 06 Nov 2016 18:17:52: 4000000
INFO @ Sun, 06 Nov 2016 18:17:53: 5000000
INFO @ Sun, 06 Nov 2016 18:17:55: 6000000
INFO @ Sun, 06 Nov 2016 18:17:57: 7000000
INFO @ Sun, 06 Nov 2016 18:17:58: 8000000
INFO @ Sun, 06 Nov 2016 18:18:00: 9000000
INFO @ Sun, 06 Nov 2016 18:18:01: 10000000
INFO @ Sun, 06 Nov 2016 18:18:02: 11000000
INFO @ Sun, 06 Nov 2016 18:18:04: 12000000
INFO @ Sun, 06 Nov 2016 18:18:05: 13000000
INFO @ Sun, 06 Nov 2016 18:18:08: 14000000
INFO @ Sun, 06 Nov 2016 18:18:10: 15000000
INFO @ Sun, 06 Nov 2016 18:18:12: 16000000
INFO @ Sun, 06 Nov 2016 18:18:14: 17000000
INFO @ Sun, 06 Nov 2016 18:18:16: 18000000
INFO @ Sun, 06 Nov 2016 18:18:17: 19000000
INFO @ Sun, 06 Nov 2016 18:18:19: 20000000
INFO @ Sun, 06 Nov 2016 18:18:20: 21000000
INFO @ Sun, 06 Nov 2016 18:18:22: 22000000
INFO @ Sun, 06 Nov 2016 18:18:24: 23000000
INFO @ Sun, 06 Nov 2016 18:18:26: 24000000
INFO @ Sun, 06 Nov 2016 18:18:27: 25000000
INFO @ Sun, 06 Nov 2016 18:18:29: 26000000
INFO @ Sun, 06 Nov 2016 18:18:30: 27000000
INFO @ Sun, 06 Nov 2016 18:18:32: 28000000
INFO @ Sun, 06 Nov 2016 18:18:34: 29000000
INFO @ Sun, 06 Nov 2016 18:18:35: 30000000
INFO @ Sun, 06 Nov 2016 18:18:37: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:18:40: 1000000
INFO @ Sun, 06 Nov 2016 18:18:41: 2000000
INFO @ Sun, 06 Nov 2016 18:18:42: 3000000
INFO @ Sun, 06 Nov 2016 18:18:43: #1 tag size is determined as 45 bps
INFO @ Sun, 06 Nov 2016 18:18:43: #1 tag size = 45
INFO @ Sun, 06 Nov 2016 18:18:43: #1 total tags in treatment: 30955688
INFO @ Sun, 06 Nov 2016 18:18:43: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:18:43: #1 finished!
INFO @ Sun, 06 Nov 2016 18:18:43: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:18:43: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:18:43: #2 Use 115 as fragment length
INFO @ Sun, 06 Nov 2016 18:18:43: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:18:43: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 06 Nov 2016 18:18:43: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:19:36: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 06 Nov 2016 18:19:36: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 06 Nov 2016 18:19:36: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 06 Nov 2016 18:19:36: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 06 Nov 2016 18:19:36: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:22:06: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:22:06: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 06 Nov 2016 18:22:06: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed
INFO @ Sun, 06 Nov 2016 18:22:06: Done!
INFO @ Sun, 06 Nov 2016 18:22:08:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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 @ Sun, 06 Nov 2016 18:22:08: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:22:08: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:22:10: 1000000
INFO @ Sun, 06 Nov 2016 18:22:11: 2000000
INFO @ Sun, 06 Nov 2016 18:22:13: 3000000
INFO @ Sun, 06 Nov 2016 18:22:14: 4000000
INFO @ Sun, 06 Nov 2016 18:22:16: 5000000
INFO @ Sun, 06 Nov 2016 18:22:17: 6000000
INFO @ Sun, 06 Nov 2016 18:22:19: 7000000
INFO @ Sun, 06 Nov 2016 18:22:20: 8000000
INFO @ Sun, 06 Nov 2016 18:22:22: 9000000
INFO @ Sun, 06 Nov 2016 18:22:23: 10000000
INFO @ Sun, 06 Nov 2016 18:22:24: 11000000
INFO @ Sun, 06 Nov 2016 18:22:26: 12000000
INFO @ Sun, 06 Nov 2016 18:22:27: 13000000
INFO @ Sun, 06 Nov 2016 18:22:29: 14000000
INFO @ Sun, 06 Nov 2016 18:22:30: 15000000
INFO @ Sun, 06 Nov 2016 18:22:31: 16000000
INFO @ Sun, 06 Nov 2016 18:22:33: 17000000
INFO @ Sun, 06 Nov 2016 18:22:34: 18000000
INFO @ Sun, 06 Nov 2016 18:22:36: 19000000
INFO @ Sun, 06 Nov 2016 18:22:37: 20000000
INFO @ Sun, 06 Nov 2016 18:22:39: 21000000
INFO @ Sun, 06 Nov 2016 18:22:40: 22000000
INFO @ Sun, 06 Nov 2016 18:22:41: 23000000
INFO @ Sun, 06 Nov 2016 18:22:43: 24000000
INFO @ Sun, 06 Nov 2016 18:22:44: 25000000
INFO @ Sun, 06 Nov 2016 18:22:46: 26000000
INFO @ Sun, 06 Nov 2016 18:22:47: 27000000
INFO @ Sun, 06 Nov 2016 18:22:49: 28000000
INFO @ Sun, 06 Nov 2016 18:22:50: 29000000
INFO @ Sun, 06 Nov 2016 18:22:51: 30000000
INFO @ Sun, 06 Nov 2016 18:22:53: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:22:55: 1000000
INFO @ Sun, 06 Nov 2016 18:22:56: 2000000
INFO @ Sun, 06 Nov 2016 18:22:57: 3000000
INFO @ Sun, 06 Nov 2016 18:22:58: #1 tag size is determined as 45 bps
INFO @ Sun, 06 Nov 2016 18:22:58: #1 tag size = 45
INFO @ Sun, 06 Nov 2016 18:22:58: #1 total tags in treatment: 30955688
INFO @ Sun, 06 Nov 2016 18:22:58: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:22:58: #1 finished!
INFO @ Sun, 06 Nov 2016 18:22:58: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:22:58: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:22:58: #2 Use 115 as fragment length
INFO @ Sun, 06 Nov 2016 18:22:58: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:22:58: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 06 Nov 2016 18:22:58: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:23:50: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:24:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:24:22: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 06 Nov 2016 18:24:22: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 06 Nov 2016 18:24:22: Done!
INFO @ Sun, 06 Nov 2016 18:24:26: Read and build treatment bedGraph...
INFO @ Sun, 06 Nov 2016 18:25:26: Read and build control bedGraph...
INFO @ Sun, 06 Nov 2016 18:25:38: Build scoreTrackII...
INFO @ Sun, 06 Nov 2016 18:26:06: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 06 Nov 2016 18:28:41: Write bedGraph of scores...
INFO @ Sun, 06 Nov 2016 18:30:37: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/rep1/ZF3_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_FE.bdg'!
Chromosome KQ030491.1 isn't in /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes line 1 of stdin
--------------------Post mortem info--------------------
==============================================================
job_number: 4357
submission_time: Sun Nov 6 18:09:26 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /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/MouseMutantData/ZF3
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/chipseq.bds.20161106_180919_110/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/MouseMutantData/ZF3/chipseq.bds.20161106_180919_110/task.callpeak_macs2.macs2_rep1.line_67.id_10.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,SGE_ROOT=/var/lib/gridengine,PATH=/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=34899.ZF3.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,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/MouseMutantData/ZF3,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 55144 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
scheduling info: queue instance "q@kadru" dropped because it is full
|
| Num | 2 | | ID | task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 | | Name | macs2 rep1-pr1 | | Thread | thread_Root | | PID | 4368 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-11-06 18:09:31 | | End | 2016-11-06 18:23:40 | | Elapsed | 00:14:09 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 69
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_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/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 88
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz
# SYS command. line 92
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
44901 (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 @ Sun, 06 Nov 2016 18:19:44:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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 @ Sun, 06 Nov 2016 18:19:44: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:19:44: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:19:47: 1000000
INFO @ Sun, 06 Nov 2016 18:19:48: 2000000
INFO @ Sun, 06 Nov 2016 18:19:50: 3000000
INFO @ Sun, 06 Nov 2016 18:19:52: 4000000
INFO @ Sun, 06 Nov 2016 18:19:54: 5000000
INFO @ Sun, 06 Nov 2016 18:19:56: 6000000
INFO @ Sun, 06 Nov 2016 18:19:57: 7000000
INFO @ Sun, 06 Nov 2016 18:19:59: 8000000
INFO @ Sun, 06 Nov 2016 18:20:00: 9000000
INFO @ Sun, 06 Nov 2016 18:20:02: 10000000
INFO @ Sun, 06 Nov 2016 18:20:03: 11000000
INFO @ Sun, 06 Nov 2016 18:20:05: 12000000
INFO @ Sun, 06 Nov 2016 18:20:07: 13000000
INFO @ Sun, 06 Nov 2016 18:20:09: 14000000
INFO @ Sun, 06 Nov 2016 18:20:10: 15000000
INFO @ Sun, 06 Nov 2016 18:20:12: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:20:14: 1000000
INFO @ Sun, 06 Nov 2016 18:20:15: 2000000
INFO @ Sun, 06 Nov 2016 18:20:17: 3000000
INFO @ Sun, 06 Nov 2016 18:20:18: #1 tag size is determined as 48 bps
INFO @ Sun, 06 Nov 2016 18:20:18: #1 tag size = 48
INFO @ Sun, 06 Nov 2016 18:20:18: #1 total tags in treatment: 15477844
INFO @ Sun, 06 Nov 2016 18:20:18: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:20:18: #1 finished!
INFO @ Sun, 06 Nov 2016 18:20:18: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:20:18: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:20:18: #2 Use 115 as fragment length
INFO @ Sun, 06 Nov 2016 18:20:18: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:20:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 06 Nov 2016 18:20:18: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:20:51: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 06 Nov 2016 18:20:51: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 06 Nov 2016 18:20:51: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 06 Nov 2016 18:20:51: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 06 Nov 2016 18:20:51: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:22:17: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:22:17: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 06 Nov 2016 18:22:17: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed
INFO @ Sun, 06 Nov 2016 18:22:18: Done!
INFO @ Sun, 06 Nov 2016 18:22:21:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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 @ Sun, 06 Nov 2016 18:22:21: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:22:21: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:22:23: 1000000
INFO @ Sun, 06 Nov 2016 18:22:24: 2000000
INFO @ Sun, 06 Nov 2016 18:22:26: 3000000
INFO @ Sun, 06 Nov 2016 18:22:27: 4000000
INFO @ Sun, 06 Nov 2016 18:22:29: 5000000
INFO @ Sun, 06 Nov 2016 18:22:30: 6000000
INFO @ Sun, 06 Nov 2016 18:22:32: 7000000
INFO @ Sun, 06 Nov 2016 18:22:33: 8000000
INFO @ Sun, 06 Nov 2016 18:22:35: 9000000
INFO @ Sun, 06 Nov 2016 18:22:36: 10000000
INFO @ Sun, 06 Nov 2016 18:22:38: 11000000
INFO @ Sun, 06 Nov 2016 18:22:39: 12000000
INFO @ Sun, 06 Nov 2016 18:22:40: 13000000
INFO @ Sun, 06 Nov 2016 18:22:42: 14000000
INFO @ Sun, 06 Nov 2016 18:22:43: 15000000
INFO @ Sun, 06 Nov 2016 18:22:45: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:22:46: 1000000
INFO @ Sun, 06 Nov 2016 18:22:48: 2000000
INFO @ Sun, 06 Nov 2016 18:22:49: 3000000
INFO @ Sun, 06 Nov 2016 18:22:50: #1 tag size is determined as 48 bps
INFO @ Sun, 06 Nov 2016 18:22:50: #1 tag size = 48
INFO @ Sun, 06 Nov 2016 18:22:50: #1 total tags in treatment: 15477844
INFO @ Sun, 06 Nov 2016 18:22:50: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:22:50: #1 finished!
INFO @ Sun, 06 Nov 2016 18:22:50: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:22:50: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:22:50: #2 Use 115 as fragment length
INFO @ Sun, 06 Nov 2016 18:22:50: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:22:50: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 06 Nov 2016 18:22:50: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:23:17: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:23:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:23:37: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 06 Nov 2016 18:23:37: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 06 Nov 2016 18:23:37: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 4378 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-11-06 18:09:32 | | End | 2016-11-06 18:26:05 | | Elapsed | 00:16:32 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 69
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
# SYS command. line 81
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 88
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz
# SYS command. line 92
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
6085 (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 @ Sun, 06 Nov 2016 18:21:01:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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 @ Sun, 06 Nov 2016 18:21:01: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:21:01: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:21:04: 1000000
INFO @ Sun, 06 Nov 2016 18:21:06: 2000000
INFO @ Sun, 06 Nov 2016 18:21:08: 3000000
INFO @ Sun, 06 Nov 2016 18:21:10: 4000000
INFO @ Sun, 06 Nov 2016 18:21:13: 5000000
INFO @ Sun, 06 Nov 2016 18:21:15: 6000000
INFO @ Sun, 06 Nov 2016 18:21:17: 7000000
INFO @ Sun, 06 Nov 2016 18:21:19: 8000000
INFO @ Sun, 06 Nov 2016 18:21:21: 9000000
INFO @ Sun, 06 Nov 2016 18:21:23: 10000000
INFO @ Sun, 06 Nov 2016 18:21:25: 11000000
INFO @ Sun, 06 Nov 2016 18:21:27: 12000000
INFO @ Sun, 06 Nov 2016 18:21:29: 13000000
INFO @ Sun, 06 Nov 2016 18:21:31: 14000000
INFO @ Sun, 06 Nov 2016 18:21:33: 15000000
INFO @ Sun, 06 Nov 2016 18:21:35: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:21:37: 1000000
INFO @ Sun, 06 Nov 2016 18:21:38: 2000000
INFO @ Sun, 06 Nov 2016 18:21:40: 3000000
INFO @ Sun, 06 Nov 2016 18:21:41: #1 tag size is determined as 48 bps
INFO @ Sun, 06 Nov 2016 18:21:41: #1 tag size = 48
INFO @ Sun, 06 Nov 2016 18:21:41: #1 total tags in treatment: 15477844
INFO @ Sun, 06 Nov 2016 18:21:41: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:21:41: #1 finished!
INFO @ Sun, 06 Nov 2016 18:21:41: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:21:41: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:21:41: #2 Use 115 as fragment length
INFO @ Sun, 06 Nov 2016 18:21:41: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:21:41: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 06 Nov 2016 18:21:41: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:22:12: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 06 Nov 2016 18:22:12: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 06 Nov 2016 18:22:12: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 06 Nov 2016 18:22:12: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 06 Nov 2016 18:22:12: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:23:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:23:58: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 06 Nov 2016 18:23:59: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed
INFO @ Sun, 06 Nov 2016 18:23:59: Done!
INFO @ Sun, 06 Nov 2016 18:24:03:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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 @ Sun, 06 Nov 2016 18:24:03: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:24:03: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:24:07: 1000000
INFO @ Sun, 06 Nov 2016 18:24:09: 2000000
INFO @ Sun, 06 Nov 2016 18:24:11: 3000000
INFO @ Sun, 06 Nov 2016 18:24:13: 4000000
INFO @ Sun, 06 Nov 2016 18:24:15: 5000000
INFO @ Sun, 06 Nov 2016 18:24:17: 6000000
INFO @ Sun, 06 Nov 2016 18:24:19: 7000000
INFO @ Sun, 06 Nov 2016 18:24:21: 8000000
INFO @ Sun, 06 Nov 2016 18:24:23: 9000000
INFO @ Sun, 06 Nov 2016 18:24:25: 10000000
INFO @ Sun, 06 Nov 2016 18:24:27: 11000000
INFO @ Sun, 06 Nov 2016 18:24:30: 12000000
INFO @ Sun, 06 Nov 2016 18:24:33: 13000000
INFO @ Sun, 06 Nov 2016 18:24:35: 14000000
INFO @ Sun, 06 Nov 2016 18:24:37: 15000000
INFO @ Sun, 06 Nov 2016 18:24:40: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:24:42: 1000000
INFO @ Sun, 06 Nov 2016 18:24:44: 2000000
INFO @ Sun, 06 Nov 2016 18:24:46: 3000000
INFO @ Sun, 06 Nov 2016 18:24:47: #1 tag size is determined as 48 bps
INFO @ Sun, 06 Nov 2016 18:24:47: #1 tag size = 48
INFO @ Sun, 06 Nov 2016 18:24:47: #1 total tags in treatment: 15477844
INFO @ Sun, 06 Nov 2016 18:24:47: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:24:47: #1 finished!
INFO @ Sun, 06 Nov 2016 18:24:47: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:24:47: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:24:47: #2 Use 115 as fragment length
INFO @ Sun, 06 Nov 2016 18:24:47: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:24:47: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 06 Nov 2016 18:24:47: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:25:27: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:25:51: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:25:53: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 06 Nov 2016 18:25:55: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/macs2/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 06 Nov 2016 18:25:59: Done!
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