| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 4359 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-11-06 18:09:27 | | End | 2016-11-06 18:09:27 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/signal/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/signal/macs2/rep1/ZF2_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/ZF2/out/align/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/align/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1 -o "ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/signal/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/align/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1 -o "ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/signal/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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--------------------
3856 (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 18:17:47:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/rep1/ZF2_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 18:17:47: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:17:47: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:17:50: 1000000
INFO @ Sun, 06 Nov 2016 18:17:52: 2000000
INFO @ Sun, 06 Nov 2016 18:17:55: 3000000
INFO @ Sun, 06 Nov 2016 18:17:58: 4000000
INFO @ Sun, 06 Nov 2016 18:17:59: 5000000
INFO @ Sun, 06 Nov 2016 18:18:01: 6000000
INFO @ Sun, 06 Nov 2016 18:18:05: 7000000
INFO @ Sun, 06 Nov 2016 18:18:08: 8000000
INFO @ Sun, 06 Nov 2016 18:18:10: 9000000
INFO @ Sun, 06 Nov 2016 18:18:17: 10000000
INFO @ Sun, 06 Nov 2016 18:18:20: 11000000
INFO @ Sun, 06 Nov 2016 18:18:23: 12000000
INFO @ Sun, 06 Nov 2016 18:18:27: 13000000
INFO @ Sun, 06 Nov 2016 18:18:30: 14000000
INFO @ Sun, 06 Nov 2016 18:18:33: 15000000
INFO @ Sun, 06 Nov 2016 18:18:35: 16000000
INFO @ Sun, 06 Nov 2016 18:18:37: 17000000
INFO @ Sun, 06 Nov 2016 18:18:39: 18000000
INFO @ Sun, 06 Nov 2016 18:18:42: 19000000
INFO @ Sun, 06 Nov 2016 18:18:45: 20000000
INFO @ Sun, 06 Nov 2016 18:18:48: 21000000
INFO @ Sun, 06 Nov 2016 18:18:51: 22000000
INFO @ Sun, 06 Nov 2016 18:18:54: 23000000
INFO @ Sun, 06 Nov 2016 18:18:57: 24000000
INFO @ Sun, 06 Nov 2016 18:19:02: 25000000
INFO @ Sun, 06 Nov 2016 18:19:04: 26000000
INFO @ Sun, 06 Nov 2016 18:19:09: 27000000
INFO @ Sun, 06 Nov 2016 18:19:15: 28000000
INFO @ Sun, 06 Nov 2016 18:19:17: 29000000
INFO @ Sun, 06 Nov 2016 18:19:18: 30000000
INFO @ Sun, 06 Nov 2016 18:19:21: 31000000
INFO @ Sun, 06 Nov 2016 18:19:23: 32000000
INFO @ Sun, 06 Nov 2016 18:19:25: 33000000
INFO @ Sun, 06 Nov 2016 18:19:29: 34000000
INFO @ Sun, 06 Nov 2016 18:19:33: 35000000
INFO @ Sun, 06 Nov 2016 18:19:36: 36000000
INFO @ Sun, 06 Nov 2016 18:19:38: 37000000
INFO @ Sun, 06 Nov 2016 18:19:40: 38000000
INFO @ Sun, 06 Nov 2016 18:19:42: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:19:45: 1000000
INFO @ Sun, 06 Nov 2016 18:19:47: 2000000
INFO @ Sun, 06 Nov 2016 18:19:49: 3000000
INFO @ Sun, 06 Nov 2016 18:19:50: #1 tag size is determined as 42 bps
INFO @ Sun, 06 Nov 2016 18:19:50: #1 tag size = 42
INFO @ Sun, 06 Nov 2016 18:19:50: #1 total tags in treatment: 38857640
INFO @ Sun, 06 Nov 2016 18:19:50: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:19:50: #1 finished!
INFO @ Sun, 06 Nov 2016 18:19:50: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:19:50: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:19:50: #2 Use 140 as fragment length
INFO @ Sun, 06 Nov 2016 18:19:50: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:19:50: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 06 Nov 2016 18:19:50: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:20:56: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 06 Nov 2016 18:20:56: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 06 Nov 2016 18:20:56: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 06 Nov 2016 18:20:56: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 06 Nov 2016 18:20:56: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:24:35: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:24:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 06 Nov 2016 18:24:38: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed
INFO @ Sun, 06 Nov 2016 18:24:39: Done!
INFO @ Sun, 06 Nov 2016 18:24:44:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/rep1/ZF2_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/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/rep1/ZF2_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 18:24:44: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:24:44: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:24:46: 1000000
INFO @ Sun, 06 Nov 2016 18:24:48: 2000000
INFO @ Sun, 06 Nov 2016 18:24:50: 3000000
INFO @ Sun, 06 Nov 2016 18:24:52: 4000000
INFO @ Sun, 06 Nov 2016 18:24:53: 5000000
INFO @ Sun, 06 Nov 2016 18:24:55: 6000000
INFO @ Sun, 06 Nov 2016 18:24:57: 7000000
INFO @ Sun, 06 Nov 2016 18:24:59: 8000000
INFO @ Sun, 06 Nov 2016 18:25:01: 9000000
INFO @ Sun, 06 Nov 2016 18:25:03: 10000000
INFO @ Sun, 06 Nov 2016 18:25:05: 11000000
INFO @ Sun, 06 Nov 2016 18:25:07: 12000000
INFO @ Sun, 06 Nov 2016 18:25:09: 13000000
INFO @ Sun, 06 Nov 2016 18:25:11: 14000000
INFO @ Sun, 06 Nov 2016 18:25:13: 15000000
INFO @ Sun, 06 Nov 2016 18:25:15: 16000000
INFO @ Sun, 06 Nov 2016 18:25:17: 17000000
INFO @ Sun, 06 Nov 2016 18:25:19: 18000000
INFO @ Sun, 06 Nov 2016 18:25:20: 19000000
INFO @ Sun, 06 Nov 2016 18:25:22: 20000000
INFO @ Sun, 06 Nov 2016 18:25:24: 21000000
INFO @ Sun, 06 Nov 2016 18:25:26: 22000000
INFO @ Sun, 06 Nov 2016 18:25:28: 23000000
INFO @ Sun, 06 Nov 2016 18:25:30: 24000000
INFO @ Sun, 06 Nov 2016 18:25:32: 25000000
INFO @ Sun, 06 Nov 2016 18:25:33: 26000000
INFO @ Sun, 06 Nov 2016 18:25:35: 27000000
INFO @ Sun, 06 Nov 2016 18:25:37: 28000000
INFO @ Sun, 06 Nov 2016 18:25:39: 29000000
INFO @ Sun, 06 Nov 2016 18:25:41: 30000000
INFO @ Sun, 06 Nov 2016 18:25:43: 31000000
INFO @ Sun, 06 Nov 2016 18:25:45: 32000000
INFO @ Sun, 06 Nov 2016 18:25:46: 33000000
INFO @ Sun, 06 Nov 2016 18:25:48: 34000000
INFO @ Sun, 06 Nov 2016 18:25:50: 35000000
INFO @ Sun, 06 Nov 2016 18:25:52: 36000000
INFO @ Sun, 06 Nov 2016 18:25:54: 37000000
INFO @ Sun, 06 Nov 2016 18:25:56: 38000000
INFO @ Sun, 06 Nov 2016 18:25:58: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:26:02: 1000000
INFO @ Sun, 06 Nov 2016 18:26:04: 2000000
INFO @ Sun, 06 Nov 2016 18:26:05: 3000000
INFO @ Sun, 06 Nov 2016 18:26:06: #1 tag size is determined as 42 bps
INFO @ Sun, 06 Nov 2016 18:26:06: #1 tag size = 42
INFO @ Sun, 06 Nov 2016 18:26:06: #1 total tags in treatment: 38857640
INFO @ Sun, 06 Nov 2016 18:26:06: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:26:06: #1 finished!
INFO @ Sun, 06 Nov 2016 18:26:06: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:26:06: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:26:06: #2 Use 140 as fragment length
INFO @ Sun, 06 Nov 2016 18:26:06: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:26:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 06 Nov 2016 18:26:06: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:27:08: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:27:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:28:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 06 Nov 2016 18:28:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 06 Nov 2016 18:28:01: Done!
INFO @ Sun, 06 Nov 2016 18:28:06: Read and build treatment bedGraph...
INFO @ Sun, 06 Nov 2016 18:29:32: Read and build control bedGraph...
INFO @ Sun, 06 Nov 2016 18:29:46: Build scoreTrackII...
INFO @ Sun, 06 Nov 2016 18:30:14: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 06 Nov 2016 18:33:59: Write bedGraph of scores...
INFO @ Sun, 06 Nov 2016 18:36:19: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/rep1/ZF2_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: 4359
submission_time: Sun Nov 6 18:09:27 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/ZF2
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/chipseq.bds.20161106_180919_302/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/ZF2/chipseq.bds.20161106_180919_302/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=34778.ZF2.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/ZF2,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 | 4364 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-11-06 18:09:30 | | End | 2016-11-06 18:24:02 | | Elapsed | 00:14:31 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_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--------------------
44308 (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 18:19:18:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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 18:19:18: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:19:18: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:19:20: 1000000
INFO @ Sun, 06 Nov 2016 18:19:22: 2000000
INFO @ Sun, 06 Nov 2016 18:19:24: 3000000
INFO @ Sun, 06 Nov 2016 18:19:25: 4000000
INFO @ Sun, 06 Nov 2016 18:19:27: 5000000
INFO @ Sun, 06 Nov 2016 18:19:29: 6000000
INFO @ Sun, 06 Nov 2016 18:19:30: 7000000
INFO @ Sun, 06 Nov 2016 18:19:32: 8000000
INFO @ Sun, 06 Nov 2016 18:19:34: 9000000
INFO @ Sun, 06 Nov 2016 18:19:35: 10000000
INFO @ Sun, 06 Nov 2016 18:19:37: 11000000
INFO @ Sun, 06 Nov 2016 18:19:38: 12000000
INFO @ Sun, 06 Nov 2016 18:19:40: 13000000
INFO @ Sun, 06 Nov 2016 18:19:41: 14000000
INFO @ Sun, 06 Nov 2016 18:19:43: 15000000
INFO @ Sun, 06 Nov 2016 18:19:45: 16000000
INFO @ Sun, 06 Nov 2016 18:19:47: 17000000
INFO @ Sun, 06 Nov 2016 18:19:48: 18000000
INFO @ Sun, 06 Nov 2016 18:19:50: 19000000
INFO @ Sun, 06 Nov 2016 18:19:53: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:19:54: 1000000
INFO @ Sun, 06 Nov 2016 18:19:55: 2000000
INFO @ Sun, 06 Nov 2016 18:19:57: 3000000
INFO @ Sun, 06 Nov 2016 18:19:57: #1 tag size is determined as 42 bps
INFO @ Sun, 06 Nov 2016 18:19:57: #1 tag size = 42
INFO @ Sun, 06 Nov 2016 18:19:57: #1 total tags in treatment: 19428820
INFO @ Sun, 06 Nov 2016 18:19:57: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:19:57: #1 finished!
INFO @ Sun, 06 Nov 2016 18:19:57: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:19:57: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:19:57: #2 Use 140 as fragment length
INFO @ Sun, 06 Nov 2016 18:19:57: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:19:57: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 06 Nov 2016 18:19:57: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:20:25: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 06 Nov 2016 18:20:25: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 06 Nov 2016 18:20:25: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 06 Nov 2016 18:20:25: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 06 Nov 2016 18:20:25: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:22:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:22:08: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 06 Nov 2016 18:22:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed
INFO @ Sun, 06 Nov 2016 18:22:09: Done!
INFO @ Sun, 06 Nov 2016 18:22:12:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr1/ZF2_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 18:22:12: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:22:12: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:22:13: 1000000
INFO @ Sun, 06 Nov 2016 18:22:15: 2000000
INFO @ Sun, 06 Nov 2016 18:22:16: 3000000
INFO @ Sun, 06 Nov 2016 18:22:18: 4000000
INFO @ Sun, 06 Nov 2016 18:22:19: 5000000
INFO @ Sun, 06 Nov 2016 18:22:21: 6000000
INFO @ Sun, 06 Nov 2016 18:22:22: 7000000
INFO @ Sun, 06 Nov 2016 18:22:23: 8000000
INFO @ Sun, 06 Nov 2016 18:22:25: 9000000
INFO @ Sun, 06 Nov 2016 18:22:26: 10000000
INFO @ Sun, 06 Nov 2016 18:22:28: 11000000
INFO @ Sun, 06 Nov 2016 18:22:29: 12000000
INFO @ Sun, 06 Nov 2016 18:22:31: 13000000
INFO @ Sun, 06 Nov 2016 18:22:32: 14000000
INFO @ Sun, 06 Nov 2016 18:22:34: 15000000
INFO @ Sun, 06 Nov 2016 18:22:35: 16000000
INFO @ Sun, 06 Nov 2016 18:22:37: 17000000
INFO @ Sun, 06 Nov 2016 18:22:38: 18000000
INFO @ Sun, 06 Nov 2016 18:22:40: 19000000
INFO @ Sun, 06 Nov 2016 18:22:42: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:22:43: 1000000
INFO @ Sun, 06 Nov 2016 18:22:45: 2000000
INFO @ Sun, 06 Nov 2016 18:22:46: 3000000
INFO @ Sun, 06 Nov 2016 18:22:47: #1 tag size is determined as 42 bps
INFO @ Sun, 06 Nov 2016 18:22:47: #1 tag size = 42
INFO @ Sun, 06 Nov 2016 18:22:47: #1 total tags in treatment: 19428820
INFO @ Sun, 06 Nov 2016 18:22:47: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:22:47: #1 finished!
INFO @ Sun, 06 Nov 2016 18:22:47: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:22:47: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:22:47: #2 Use 140 as fragment length
INFO @ Sun, 06 Nov 2016 18:22:47: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:22:47: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 06 Nov 2016 18:22:47: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:23:25: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:23:57: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:23:58: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 06 Nov 2016 18:23:58: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr1/ZF2_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 06 Nov 2016 18:23:59: Done!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 4367 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2016-11-06 18:09:31 | | End | 2016-11-06 18:24:27 | | Elapsed | 00:14:56 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 100
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_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--------------------
2844 (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/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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 18:19:44: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:19:44: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:19:46: 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 18:19:55: 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 18:20:04: 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 18:20:11: 15000000
INFO @ Sun, 06 Nov 2016 18:20:13: 16000000
INFO @ Sun, 06 Nov 2016 18:20:14: 17000000
INFO @ Sun, 06 Nov 2016 18:20:16: 18000000
INFO @ Sun, 06 Nov 2016 18:20:18: 19000000
INFO @ Sun, 06 Nov 2016 18:20:20: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:20:22: 1000000
INFO @ Sun, 06 Nov 2016 18:20:23: 2000000
INFO @ Sun, 06 Nov 2016 18:20:25: 3000000
INFO @ Sun, 06 Nov 2016 18:20:26: #1 tag size is determined as 41 bps
INFO @ Sun, 06 Nov 2016 18:20:26: #1 tag size = 41
INFO @ Sun, 06 Nov 2016 18:20:26: #1 total tags in treatment: 19428820
INFO @ Sun, 06 Nov 2016 18:20:26: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:20:26: #1 finished!
INFO @ Sun, 06 Nov 2016 18:20:26: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:20:26: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:20:26: #2 Use 140 as fragment length
INFO @ Sun, 06 Nov 2016 18:20:26: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:20:26: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 06 Nov 2016 18:20:26: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:20:56: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 06 Nov 2016 18:20:56: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 06 Nov 2016 18:20:56: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 06 Nov 2016 18:20:56: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 06 Nov 2016 18:20:56: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:22:37: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 18:22:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 06 Nov 2016 18:22:38: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed
INFO @ Sun, 06 Nov 2016 18:22:38: Done!
INFO @ Sun, 06 Nov 2016 18:22:42:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/align/pseudo_reps/rep1/pr2/ZF2_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 18:22:42: #1 read tag files...
INFO @ Sun, 06 Nov 2016 18:22:42: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 18:22:44: 1000000
INFO @ Sun, 06 Nov 2016 18:22:45: 2000000
INFO @ Sun, 06 Nov 2016 18:22:47: 3000000
INFO @ Sun, 06 Nov 2016 18:22:49: 4000000
INFO @ Sun, 06 Nov 2016 18:22:51: 5000000
INFO @ Sun, 06 Nov 2016 18:22:53: 6000000
INFO @ Sun, 06 Nov 2016 18:22:55: 7000000
INFO @ Sun, 06 Nov 2016 18:22:57: 8000000
INFO @ Sun, 06 Nov 2016 18:22:59: 9000000
INFO @ Sun, 06 Nov 2016 18:23:01: 10000000
INFO @ Sun, 06 Nov 2016 18:23:03: 11000000
INFO @ Sun, 06 Nov 2016 18:23:05: 12000000
INFO @ Sun, 06 Nov 2016 18:23:07: 13000000
INFO @ Sun, 06 Nov 2016 18:23:09: 14000000
INFO @ Sun, 06 Nov 2016 18:23:11: 15000000
INFO @ Sun, 06 Nov 2016 18:23:13: 16000000
INFO @ Sun, 06 Nov 2016 18:23:14: 17000000
INFO @ Sun, 06 Nov 2016 18:23:16: 18000000
INFO @ Sun, 06 Nov 2016 18:23:18: 19000000
INFO @ Sun, 06 Nov 2016 18:23:20: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 18:23:22: 1000000
INFO @ Sun, 06 Nov 2016 18:23:23: 2000000
INFO @ Sun, 06 Nov 2016 18:23:25: 3000000
INFO @ Sun, 06 Nov 2016 18:23:25: #1 tag size is determined as 41 bps
INFO @ Sun, 06 Nov 2016 18:23:25: #1 tag size = 41
INFO @ Sun, 06 Nov 2016 18:23:25: #1 total tags in treatment: 19428820
INFO @ Sun, 06 Nov 2016 18:23:25: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 18:23:25: #1 finished!
INFO @ Sun, 06 Nov 2016 18:23:25: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 18:23:25: #2 Skipped...
INFO @ Sun, 06 Nov 2016 18:23:25: #2 Use 140 as fragment length
INFO @ Sun, 06 Nov 2016 18:23:25: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 18:23:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 06 Nov 2016 18:23:25: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 18:23:53: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 18:24:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.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/ZF2/out/peak/macs2/pseudo_reps/rep1/pr2/ZF2_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 06 Nov 2016 18:24:23: Done!
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