| Num | 1 | | ID | task.callpeak_macs2.macs2_rep1.line_67.id_10 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 4402 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-11-06 21:27:38 | | End | 2016-11-06 21:27:38 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/signal/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/signal/macs2/rep1/ZF5_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/ZF5/out/align/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 95 --keep-dup all -B --SPMR
# SYS command. line 78
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/align/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 95 --keep-dup all
# SYS command. line 91
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
# SYS command. line 95
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed
# SYS command. line 100
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1 -o "ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_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 $0}' | bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/signal/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_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",$1}')
# SYS command. line 130
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1 -o "ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/signal/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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--------------------
14591 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 06 Nov 2016 21:27:46:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 95 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_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 21:27:46: #1 read tag files...
INFO @ Sun, 06 Nov 2016 21:27:46: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 21:27:48: 1000000
INFO @ Sun, 06 Nov 2016 21:27:49: 2000000
INFO @ Sun, 06 Nov 2016 21:27:51: 3000000
INFO @ Sun, 06 Nov 2016 21:27:53: 4000000
INFO @ Sun, 06 Nov 2016 21:27:54: 5000000
INFO @ Sun, 06 Nov 2016 21:27:56: 6000000
INFO @ Sun, 06 Nov 2016 21:27:57: 7000000
INFO @ Sun, 06 Nov 2016 21:27:59: 8000000
INFO @ Sun, 06 Nov 2016 21:28:00: 9000000
INFO @ Sun, 06 Nov 2016 21:28:02: 10000000
INFO @ Sun, 06 Nov 2016 21:28:04: 11000000
INFO @ Sun, 06 Nov 2016 21:28:05: 12000000
INFO @ Sun, 06 Nov 2016 21:28:07: 13000000
INFO @ Sun, 06 Nov 2016 21:28:08: 14000000
INFO @ Sun, 06 Nov 2016 21:28:10: 15000000
INFO @ Sun, 06 Nov 2016 21:28:12: 16000000
INFO @ Sun, 06 Nov 2016 21:28:13: 17000000
INFO @ Sun, 06 Nov 2016 21:28:15: 18000000
INFO @ Sun, 06 Nov 2016 21:28:16: 19000000
INFO @ Sun, 06 Nov 2016 21:28:18: 20000000
INFO @ Sun, 06 Nov 2016 21:28:19: 21000000
INFO @ Sun, 06 Nov 2016 21:28:21: 22000000
INFO @ Sun, 06 Nov 2016 21:28:22: 23000000
INFO @ Sun, 06 Nov 2016 21:28:24: 24000000
INFO @ Sun, 06 Nov 2016 21:28:25: 25000000
INFO @ Sun, 06 Nov 2016 21:28:27: 26000000
INFO @ Sun, 06 Nov 2016 21:28:28: 27000000
INFO @ Sun, 06 Nov 2016 21:28:30: 28000000
INFO @ Sun, 06 Nov 2016 21:28:31: 29000000
INFO @ Sun, 06 Nov 2016 21:28:33: 30000000
INFO @ Sun, 06 Nov 2016 21:28:34: 31000000
INFO @ Sun, 06 Nov 2016 21:28:36: 32000000
INFO @ Sun, 06 Nov 2016 21:28:37: 33000000
INFO @ Sun, 06 Nov 2016 21:28:39: 34000000
INFO @ Sun, 06 Nov 2016 21:28:40: 35000000
INFO @ Sun, 06 Nov 2016 21:28:42: 36000000
INFO @ Sun, 06 Nov 2016 21:28:43: 37000000
INFO @ Sun, 06 Nov 2016 21:28:45: 38000000
INFO @ Sun, 06 Nov 2016 21:28:46: 39000000
INFO @ Sun, 06 Nov 2016 21:28:48: 40000000
INFO @ Sun, 06 Nov 2016 21:28:49: 41000000
INFO @ Sun, 06 Nov 2016 21:28:51: 42000000
INFO @ Sun, 06 Nov 2016 21:28:53: 43000000
INFO @ Sun, 06 Nov 2016 21:28:54: 44000000
INFO @ Sun, 06 Nov 2016 21:28:56: 45000000
INFO @ Sun, 06 Nov 2016 21:28:57: 46000000
INFO @ Sun, 06 Nov 2016 21:28:59: 47000000
INFO @ Sun, 06 Nov 2016 21:29:00: 48000000
INFO @ Sun, 06 Nov 2016 21:29:02: 49000000
INFO @ Sun, 06 Nov 2016 21:29:03: 50000000
INFO @ Sun, 06 Nov 2016 21:29:05: 51000000
INFO @ Sun, 06 Nov 2016 21:29:06: 52000000
INFO @ Sun, 06 Nov 2016 21:29:08: 53000000
INFO @ Sun, 06 Nov 2016 21:29:10: 54000000
INFO @ Sun, 06 Nov 2016 21:29:11: 55000000
INFO @ Sun, 06 Nov 2016 21:29:13: 56000000
INFO @ Sun, 06 Nov 2016 21:29:14: 57000000
INFO @ Sun, 06 Nov 2016 21:29:16: 58000000
INFO @ Sun, 06 Nov 2016 21:29:17: 59000000
INFO @ Sun, 06 Nov 2016 21:29:19: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 21:29:20: 1000000
INFO @ Sun, 06 Nov 2016 21:29:22: 2000000
INFO @ Sun, 06 Nov 2016 21:29:24: 3000000
INFO @ Sun, 06 Nov 2016 21:29:24: #1 tag size is determined as 49 bps
INFO @ Sun, 06 Nov 2016 21:29:24: #1 tag size = 49
INFO @ Sun, 06 Nov 2016 21:29:24: #1 total tags in treatment: 59491042
INFO @ Sun, 06 Nov 2016 21:29:24: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 21:29:24: #1 finished!
INFO @ Sun, 06 Nov 2016 21:29:24: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 21:29:24: #2 Skipped...
INFO @ Sun, 06 Nov 2016 21:29:24: #2 Use 95 as fragment length
INFO @ Sun, 06 Nov 2016 21:29:24: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 21:29:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 06 Nov 2016 21:29:24: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 21:30:35: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 06 Nov 2016 21:30:35: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 06 Nov 2016 21:30:35: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 06 Nov 2016 21:30:35: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 06 Nov 2016 21:30:35: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 21:34:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 21:34:27: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 06 Nov 2016 21:34:27: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed
INFO @ Sun, 06 Nov 2016 21:34:28: Done!
INFO @ Sun, 06 Nov 2016 21:34:30:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_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/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 95 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_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 21:34:30: #1 read tag files...
INFO @ Sun, 06 Nov 2016 21:34:30: #1 read treatment tags...
INFO @ Sun, 06 Nov 2016 21:34:32: 1000000
INFO @ Sun, 06 Nov 2016 21:34:33: 2000000
INFO @ Sun, 06 Nov 2016 21:34:35: 3000000
INFO @ Sun, 06 Nov 2016 21:34:37: 4000000
INFO @ Sun, 06 Nov 2016 21:34:38: 5000000
INFO @ Sun, 06 Nov 2016 21:34:40: 6000000
INFO @ Sun, 06 Nov 2016 21:34:41: 7000000
INFO @ Sun, 06 Nov 2016 21:34:43: 8000000
INFO @ Sun, 06 Nov 2016 21:34:44: 9000000
INFO @ Sun, 06 Nov 2016 21:34:46: 10000000
INFO @ Sun, 06 Nov 2016 21:34:48: 11000000
INFO @ Sun, 06 Nov 2016 21:34:49: 12000000
INFO @ Sun, 06 Nov 2016 21:34:51: 13000000
INFO @ Sun, 06 Nov 2016 21:34:52: 14000000
INFO @ Sun, 06 Nov 2016 21:34:54: 15000000
INFO @ Sun, 06 Nov 2016 21:34:55: 16000000
INFO @ Sun, 06 Nov 2016 21:34:57: 17000000
INFO @ Sun, 06 Nov 2016 21:34:58: 18000000
INFO @ Sun, 06 Nov 2016 21:35:00: 19000000
INFO @ Sun, 06 Nov 2016 21:35:02: 20000000
INFO @ Sun, 06 Nov 2016 21:35:03: 21000000
INFO @ Sun, 06 Nov 2016 21:35:05: 22000000
INFO @ Sun, 06 Nov 2016 21:35:06: 23000000
INFO @ Sun, 06 Nov 2016 21:35:08: 24000000
INFO @ Sun, 06 Nov 2016 21:35:09: 25000000
INFO @ Sun, 06 Nov 2016 21:35:11: 26000000
INFO @ Sun, 06 Nov 2016 21:35:13: 27000000
INFO @ Sun, 06 Nov 2016 21:35:15: 28000000
INFO @ Sun, 06 Nov 2016 21:35:16: 29000000
INFO @ Sun, 06 Nov 2016 21:35:18: 30000000
INFO @ Sun, 06 Nov 2016 21:35:20: 31000000
INFO @ Sun, 06 Nov 2016 21:35:21: 32000000
INFO @ Sun, 06 Nov 2016 21:35:23: 33000000
INFO @ Sun, 06 Nov 2016 21:35:24: 34000000
INFO @ Sun, 06 Nov 2016 21:35:26: 35000000
INFO @ Sun, 06 Nov 2016 21:35:28: 36000000
INFO @ Sun, 06 Nov 2016 21:35:29: 37000000
INFO @ Sun, 06 Nov 2016 21:35:31: 38000000
INFO @ Sun, 06 Nov 2016 21:35:32: 39000000
INFO @ Sun, 06 Nov 2016 21:35:34: 40000000
INFO @ Sun, 06 Nov 2016 21:35:35: 41000000
INFO @ Sun, 06 Nov 2016 21:35:37: 42000000
INFO @ Sun, 06 Nov 2016 21:35:39: 43000000
INFO @ Sun, 06 Nov 2016 21:35:40: 44000000
INFO @ Sun, 06 Nov 2016 21:35:42: 45000000
INFO @ Sun, 06 Nov 2016 21:35:43: 46000000
INFO @ Sun, 06 Nov 2016 21:35:45: 47000000
INFO @ Sun, 06 Nov 2016 21:35:46: 48000000
INFO @ Sun, 06 Nov 2016 21:35:48: 49000000
INFO @ Sun, 06 Nov 2016 21:35:49: 50000000
INFO @ Sun, 06 Nov 2016 21:35:51: 51000000
INFO @ Sun, 06 Nov 2016 21:35:53: 52000000
INFO @ Sun, 06 Nov 2016 21:35:54: 53000000
INFO @ Sun, 06 Nov 2016 21:35:56: 54000000
INFO @ Sun, 06 Nov 2016 21:35:58: 55000000
INFO @ Sun, 06 Nov 2016 21:35:59: 56000000
INFO @ Sun, 06 Nov 2016 21:36:01: 57000000
INFO @ Sun, 06 Nov 2016 21:36:02: 58000000
INFO @ Sun, 06 Nov 2016 21:36:04: 59000000
INFO @ Sun, 06 Nov 2016 21:36:05: #1.2 read input tags...
INFO @ Sun, 06 Nov 2016 21:36:07: 1000000
INFO @ Sun, 06 Nov 2016 21:36:09: 2000000
INFO @ Sun, 06 Nov 2016 21:36:11: 3000000
INFO @ Sun, 06 Nov 2016 21:36:11: #1 tag size is determined as 49 bps
INFO @ Sun, 06 Nov 2016 21:36:11: #1 tag size = 49
INFO @ Sun, 06 Nov 2016 21:36:11: #1 total tags in treatment: 59491042
INFO @ Sun, 06 Nov 2016 21:36:11: #1 total tags in control: 3384182
INFO @ Sun, 06 Nov 2016 21:36:11: #1 finished!
INFO @ Sun, 06 Nov 2016 21:36:11: #2 Build Peak Model...
INFO @ Sun, 06 Nov 2016 21:36:11: #2 Skipped...
INFO @ Sun, 06 Nov 2016 21:36:11: #2 Use 95 as fragment length
INFO @ Sun, 06 Nov 2016 21:36:11: #3 Call peaks...
INFO @ Sun, 06 Nov 2016 21:36:11: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 06 Nov 2016 21:36:11: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 06 Nov 2016 21:37:15: #3 Call peaks for each chromosome...
INFO @ Sun, 06 Nov 2016 21:37:45: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls
INFO @ Sun, 06 Nov 2016 21:37:45: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 06 Nov 2016 21:37:45: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 06 Nov 2016 21:37:46: Done!
INFO @ Sun, 06 Nov 2016 21:37:48: Read and build treatment bedGraph...
INFO @ Sun, 06 Nov 2016 21:39:42: Read and build control bedGraph...
INFO @ Sun, 06 Nov 2016 21:39:54: Build scoreTrackII...
INFO @ Sun, 06 Nov 2016 21:40:30: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 06 Nov 2016 21:45:34: Write bedGraph of scores...
INFO @ Sun, 06 Nov 2016 21:49:01: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/macs2/rep1/ZF5_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: 4402
exec_file: job_scripts/4402
submission_time: Sun Nov 6 21:27:38 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/chipseq.bds.20161106_212732_233/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/ZF5/chipseq.bds.20161106_212732_233/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,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=31738.ZF5.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,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/ZF5,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:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
script_file: STDIN
usage 1: cpu=00:21:07, mem=1955.84095 GBs, io=29.55547, vmem=607.406M, maxvmem=3.988G
scheduling info: queue instance "q@kadru" dropped because it is full
|