| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
| Num | 1 | | ID | task.callpeak_spp.spp_rep1.line_57.id_10 | | Name | spp rep1 | | Thread | thread_Root | | PID | 24242 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-06 14:30:31 | | End | 2017-01-07 02:16:28 | | Elapsed | 11:45:56 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
| | Dependencies | | |
# SYS command. line 59
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 62
if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 66
Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1 -speak=140 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
# SYS command. line 72
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
# SYS command. line 74
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
# SYS command. line 77
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi
# SYS command. line 80
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 82
if [[ true == "true" ]]; then \
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
fi
# SYS command. line 86
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
4160 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 140
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: 3e+05
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz
opened /tmp/24242.1.q/Rtmp4TFTeP/SRR1370898_1.nodup.tagAlign10bb28f0b99f
done. read 4914716 fragments
ChIP data read length 69
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
opened /tmp/24242.1.q/Rtmp4TFTeP/input15MReadsNSCLess1.05.50MSubsample.tagAlign10bb6729d6ac
done. read 50000000 fragments
Control data read length 68
Calculating peak characteristics
Minimum cross-correlation value 0.06549716
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.112173807200543
Top 3 estimates for fragment length 140
Window half size 175
Phantom peak location 70
Phantom peak Correlation 0.06739866
Normalized Strand cross-correlation coefficient (NSC) 1.712651
Relative Strand cross-correlation Coefficient (RSC) 24.54722
Phantom Peak Quality Tag 2
null device
1
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 10.16759 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.09835175 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000382
Detected 188326 peaks
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1 2564 2740 . 0 . 29.8011505658887 -1 4.96087491617322 88
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1 2564 2740 . 0 . 29.8011505658887 -1 4.96087491617322 88
|
| Num | 2 | | ID | task.callpeak_macs2.macs2_rep1.line_71.id_11 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 24243 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-06 14:30:33 | | End | 2017-01-06 15:15:16 | | Elapsed | 00:44:43 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/signal/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/signal/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 110
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1 -o "SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/signal/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1 -o "SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/signal/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
29432 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Fri, 06 Jan 2017 14:30:54:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Fri, 06 Jan 2017 14:30:54: #1 read tag files...
INFO @ Fri, 06 Jan 2017 14:30:54: #1 read treatment tags...
INFO @ Fri, 06 Jan 2017 14:30:55: 1000000
INFO @ Fri, 06 Jan 2017 14:30:57: 2000000
INFO @ Fri, 06 Jan 2017 14:30:58: 3000000
INFO @ Fri, 06 Jan 2017 14:31:00: 4000000
INFO @ Fri, 06 Jan 2017 14:31:01: #1.2 read input tags...
INFO @ Fri, 06 Jan 2017 14:31:03: 1000000
INFO @ Fri, 06 Jan 2017 14:31:04: 2000000
INFO @ Fri, 06 Jan 2017 14:31:05: 3000000
INFO @ Fri, 06 Jan 2017 14:31:07: 4000000
INFO @ Fri, 06 Jan 2017 14:31:08: 5000000
INFO @ Fri, 06 Jan 2017 14:31:10: 6000000
INFO @ Fri, 06 Jan 2017 14:31:11: 7000000
INFO @ Fri, 06 Jan 2017 14:31:12: 8000000
INFO @ Fri, 06 Jan 2017 14:31:14: 9000000
INFO @ Fri, 06 Jan 2017 14:31:15: 10000000
INFO @ Fri, 06 Jan 2017 14:31:17: 11000000
INFO @ Fri, 06 Jan 2017 14:31:18: 12000000
INFO @ Fri, 06 Jan 2017 14:31:19: 13000000
INFO @ Fri, 06 Jan 2017 14:31:21: 14000000
INFO @ Fri, 06 Jan 2017 14:31:22: 15000000
INFO @ Fri, 06 Jan 2017 14:31:24: 16000000
INFO @ Fri, 06 Jan 2017 14:31:25: 17000000
INFO @ Fri, 06 Jan 2017 14:31:26: 18000000
INFO @ Fri, 06 Jan 2017 14:31:28: 19000000
INFO @ Fri, 06 Jan 2017 14:31:29: 20000000
INFO @ Fri, 06 Jan 2017 14:31:31: 21000000
INFO @ Fri, 06 Jan 2017 14:31:32: 22000000
INFO @ Fri, 06 Jan 2017 14:31:33: 23000000
INFO @ Fri, 06 Jan 2017 14:31:35: 24000000
INFO @ Fri, 06 Jan 2017 14:31:36: 25000000
INFO @ Fri, 06 Jan 2017 14:31:38: 26000000
INFO @ Fri, 06 Jan 2017 14:31:39: 27000000
INFO @ Fri, 06 Jan 2017 14:31:41: 28000000
INFO @ Fri, 06 Jan 2017 14:31:42: 29000000
INFO @ Fri, 06 Jan 2017 14:31:43: 30000000
INFO @ Fri, 06 Jan 2017 14:31:45: 31000000
INFO @ Fri, 06 Jan 2017 14:31:46: 32000000
INFO @ Fri, 06 Jan 2017 14:31:48: 33000000
INFO @ Fri, 06 Jan 2017 14:31:49: 34000000
INFO @ Fri, 06 Jan 2017 14:31:51: 35000000
INFO @ Fri, 06 Jan 2017 14:31:52: 36000000
INFO @ Fri, 06 Jan 2017 14:31:53: 37000000
INFO @ Fri, 06 Jan 2017 14:31:55: 38000000
INFO @ Fri, 06 Jan 2017 14:31:56: 39000000
INFO @ Fri, 06 Jan 2017 14:31:58: 40000000
INFO @ Fri, 06 Jan 2017 14:31:59: 41000000
INFO @ Fri, 06 Jan 2017 14:32:01: 42000000
INFO @ Fri, 06 Jan 2017 14:32:02: 43000000
INFO @ Fri, 06 Jan 2017 14:32:04: 44000000
INFO @ Fri, 06 Jan 2017 14:32:05: 45000000
INFO @ Fri, 06 Jan 2017 14:32:06: 46000000
INFO @ Fri, 06 Jan 2017 14:32:08: 47000000
INFO @ Fri, 06 Jan 2017 14:32:09: 48000000
INFO @ Fri, 06 Jan 2017 14:32:11: 49000000
INFO @ Fri, 06 Jan 2017 14:32:12: 50000000
INFO @ Fri, 06 Jan 2017 14:32:14: #1 tag size is determined as 69 bps
INFO @ Fri, 06 Jan 2017 14:32:14: #1 tag size = 69
INFO @ Fri, 06 Jan 2017 14:32:14: #1 total tags in treatment: 4914716
INFO @ Fri, 06 Jan 2017 14:32:14: #1 total tags in control: 50000000
INFO @ Fri, 06 Jan 2017 14:32:14: #1 finished!
INFO @ Fri, 06 Jan 2017 14:32:14: #2 Build Peak Model...
INFO @ Fri, 06 Jan 2017 14:32:14: #2 Skipped...
INFO @ Fri, 06 Jan 2017 14:32:14: #2 Use 140 as fragment length
INFO @ Fri, 06 Jan 2017 14:32:14: #3 Call peaks...
INFO @ Fri, 06 Jan 2017 14:32:14: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Fri, 06 Jan 2017 14:32:14: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 06 Jan 2017 14:34:39: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Fri, 06 Jan 2017 14:34:39: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Fri, 06 Jan 2017 14:34:39: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Fri, 06 Jan 2017 14:34:39: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Fri, 06 Jan 2017 14:34:39: #3 Call peaks for each chromosome...
INFO @ Fri, 06 Jan 2017 14:39:00: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Fri, 06 Jan 2017 14:39:03: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Fri, 06 Jan 2017 14:39:05: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Fri, 06 Jan 2017 14:39:07: Done!
INFO @ Fri, 06 Jan 2017 14:39:12:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/rep1/SRR1370898_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Fri, 06 Jan 2017 14:39:12: #1 read tag files...
INFO @ Fri, 06 Jan 2017 14:39:12: #1 read treatment tags...
INFO @ Fri, 06 Jan 2017 14:39:14: 1000000
INFO @ Fri, 06 Jan 2017 14:39:15: 2000000
INFO @ Fri, 06 Jan 2017 14:39:17: 3000000
INFO @ Fri, 06 Jan 2017 14:39:18: 4000000
INFO @ Fri, 06 Jan 2017 14:39:20: #1.2 read input tags...
INFO @ Fri, 06 Jan 2017 14:39:21: 1000000
INFO @ Fri, 06 Jan 2017 14:39:23: 2000000
INFO @ Fri, 06 Jan 2017 14:39:24: 3000000
INFO @ Fri, 06 Jan 2017 14:39:26: 4000000
INFO @ Fri, 06 Jan 2017 14:39:27: 5000000
INFO @ Fri, 06 Jan 2017 14:39:29: 6000000
INFO @ Fri, 06 Jan 2017 14:39:30: 7000000
INFO @ Fri, 06 Jan 2017 14:39:32: 8000000
INFO @ Fri, 06 Jan 2017 14:39:33: 9000000
INFO @ Fri, 06 Jan 2017 14:39:35: 10000000
INFO @ Fri, 06 Jan 2017 14:39:36: 11000000
INFO @ Fri, 06 Jan 2017 14:39:38: 12000000
INFO @ Fri, 06 Jan 2017 14:39:39: 13000000
INFO @ Fri, 06 Jan 2017 14:39:41: 14000000
INFO @ Fri, 06 Jan 2017 14:39:42: 15000000
INFO @ Fri, 06 Jan 2017 14:39:44: 16000000
INFO @ Fri, 06 Jan 2017 14:39:45: 17000000
INFO @ Fri, 06 Jan 2017 14:39:48: 18000000
INFO @ Fri, 06 Jan 2017 14:39:50: 19000000
INFO @ Fri, 06 Jan 2017 14:39:51: 20000000
INFO @ Fri, 06 Jan 2017 14:39:53: 21000000
INFO @ Fri, 06 Jan 2017 14:39:54: 22000000
INFO @ Fri, 06 Jan 2017 14:39:56: 23000000
INFO @ Fri, 06 Jan 2017 14:39:57: 24000000
INFO @ Fri, 06 Jan 2017 14:39:59: 25000000
INFO @ Fri, 06 Jan 2017 14:40:00: 26000000
INFO @ Fri, 06 Jan 2017 14:40:02: 27000000
INFO @ Fri, 06 Jan 2017 14:40:03: 28000000
INFO @ Fri, 06 Jan 2017 14:40:05: 29000000
INFO @ Fri, 06 Jan 2017 14:40:06: 30000000
INFO @ Fri, 06 Jan 2017 14:40:08: 31000000
INFO @ Fri, 06 Jan 2017 14:40:09: 32000000
INFO @ Fri, 06 Jan 2017 14:40:11: 33000000
INFO @ Fri, 06 Jan 2017 14:40:12: 34000000
INFO @ Fri, 06 Jan 2017 14:40:14: 35000000
INFO @ Fri, 06 Jan 2017 14:40:15: 36000000
INFO @ Fri, 06 Jan 2017 14:40:17: 37000000
INFO @ Fri, 06 Jan 2017 14:40:18: 38000000
INFO @ Fri, 06 Jan 2017 14:40:20: 39000000
INFO @ Fri, 06 Jan 2017 14:40:21: 40000000
INFO @ Fri, 06 Jan 2017 14:40:23: 41000000
INFO @ Fri, 06 Jan 2017 14:40:24: 42000000
INFO @ Fri, 06 Jan 2017 14:40:26: 43000000
INFO @ Fri, 06 Jan 2017 14:40:27: 44000000
INFO @ Fri, 06 Jan 2017 14:40:29: 45000000
INFO @ Fri, 06 Jan 2017 14:40:30: 46000000
INFO @ Fri, 06 Jan 2017 14:40:32: 47000000
INFO @ Fri, 06 Jan 2017 14:40:33: 48000000
INFO @ Fri, 06 Jan 2017 14:40:35: 49000000
INFO @ Fri, 06 Jan 2017 14:40:36: 50000000
INFO @ Fri, 06 Jan 2017 14:40:38: #1 tag size is determined as 69 bps
INFO @ Fri, 06 Jan 2017 14:40:38: #1 tag size = 69
INFO @ Fri, 06 Jan 2017 14:40:38: #1 total tags in treatment: 4914716
INFO @ Fri, 06 Jan 2017 14:40:38: #1 total tags in control: 50000000
INFO @ Fri, 06 Jan 2017 14:40:38: #1 finished!
INFO @ Fri, 06 Jan 2017 14:40:38: #2 Build Peak Model...
INFO @ Fri, 06 Jan 2017 14:40:38: #2 Skipped...
INFO @ Fri, 06 Jan 2017 14:40:38: #2 Use 140 as fragment length
INFO @ Fri, 06 Jan 2017 14:40:38: #3 Call peaks...
INFO @ Fri, 06 Jan 2017 14:40:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Fri, 06 Jan 2017 14:40:38: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 06 Jan 2017 14:43:03: #3 Call peaks for each chromosome...
INFO @ Fri, 06 Jan 2017 14:45:51: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Fri, 06 Jan 2017 14:46:02: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Fri, 06 Jan 2017 14:46:09: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Fri, 06 Jan 2017 14:46:15: Done!
INFO @ Fri, 06 Jan 2017 14:46:36: Read and build treatment bedGraph...
INFO @ Fri, 06 Jan 2017 14:46:47: Read and build control bedGraph...
INFO @ Fri, 06 Jan 2017 14:48:36: Build scoreTrackII...
INFO @ Fri, 06 Jan 2017 14:49:10: Calculate scores comparing treatment and control by 'FE'...
INFO @ Fri, 06 Jan 2017 14:53:25: Write bedGraph of scores...
INFO @ Fri, 06 Jan 2017 14:54:36: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'!
INFO @ Fri, 06 Jan 2017 14:57:01: Read and build treatment bedGraph...
INFO @ Fri, 06 Jan 2017 14:57:11: Read and build control bedGraph...
INFO @ Fri, 06 Jan 2017 14:58:59: Build scoreTrackII...
INFO @ Fri, 06 Jan 2017 14:59:32: Values in your input bedGraph files will be multiplied by 4.914716 ...
INFO @ Fri, 06 Jan 2017 15:04:09: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Fri, 06 Jan 2017 15:04:42: Write bedGraph of scores...
INFO @ Fri, 06 Jan 2017 15:07:21: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'!
|
| Num | 3 | | ID | task.callpeak_macs2.macs2_rep1_pr1.line_71.id_12 | | Name | macs2 rep1-pr1 | | Thread | thread_Root | | PID | 24244 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-06 14:30:36 | | End | 2017-01-06 14:48:39 | | Elapsed | 00:18:03 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
4161 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Fri, 06 Jan 2017 14:30:53:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Fri, 06 Jan 2017 14:30:53: #1 read tag files...
INFO @ Fri, 06 Jan 2017 14:30:53: #1 read treatment tags...
INFO @ Fri, 06 Jan 2017 14:30:55: 1000000
INFO @ Fri, 06 Jan 2017 14:30:57: 2000000
INFO @ Fri, 06 Jan 2017 14:30:58: #1.2 read input tags...
INFO @ Fri, 06 Jan 2017 14:31:01: 1000000
INFO @ Fri, 06 Jan 2017 14:31:02: 2000000
INFO @ Fri, 06 Jan 2017 14:31:04: 3000000
INFO @ Fri, 06 Jan 2017 14:31:06: 4000000
INFO @ Fri, 06 Jan 2017 14:31:07: 5000000
INFO @ Fri, 06 Jan 2017 14:31:09: 6000000
INFO @ Fri, 06 Jan 2017 14:31:11: 7000000
INFO @ Fri, 06 Jan 2017 14:31:13: 8000000
INFO @ Fri, 06 Jan 2017 14:31:15: 9000000
INFO @ Fri, 06 Jan 2017 14:31:16: 10000000
INFO @ Fri, 06 Jan 2017 14:31:18: 11000000
INFO @ Fri, 06 Jan 2017 14:31:19: 12000000
INFO @ Fri, 06 Jan 2017 14:31:21: 13000000
INFO @ Fri, 06 Jan 2017 14:31:23: 14000000
INFO @ Fri, 06 Jan 2017 14:31:24: 15000000
INFO @ Fri, 06 Jan 2017 14:31:26: 16000000
INFO @ Fri, 06 Jan 2017 14:31:27: 17000000
INFO @ Fri, 06 Jan 2017 14:31:29: 18000000
INFO @ Fri, 06 Jan 2017 14:31:31: 19000000
INFO @ Fri, 06 Jan 2017 14:31:32: 20000000
INFO @ Fri, 06 Jan 2017 14:31:34: 21000000
INFO @ Fri, 06 Jan 2017 14:31:36: 22000000
INFO @ Fri, 06 Jan 2017 14:31:37: 23000000
INFO @ Fri, 06 Jan 2017 14:31:39: 24000000
INFO @ Fri, 06 Jan 2017 14:31:40: 25000000
INFO @ Fri, 06 Jan 2017 14:31:42: 26000000
INFO @ Fri, 06 Jan 2017 14:31:44: 27000000
INFO @ Fri, 06 Jan 2017 14:31:45: 28000000
INFO @ Fri, 06 Jan 2017 14:31:47: 29000000
INFO @ Fri, 06 Jan 2017 14:31:49: 30000000
INFO @ Fri, 06 Jan 2017 14:31:50: 31000000
INFO @ Fri, 06 Jan 2017 14:31:52: 32000000
INFO @ Fri, 06 Jan 2017 14:31:54: 33000000
INFO @ Fri, 06 Jan 2017 14:31:55: 34000000
INFO @ Fri, 06 Jan 2017 14:31:57: 35000000
INFO @ Fri, 06 Jan 2017 14:31:58: 36000000
INFO @ Fri, 06 Jan 2017 14:32:00: 37000000
INFO @ Fri, 06 Jan 2017 14:32:02: 38000000
INFO @ Fri, 06 Jan 2017 14:32:03: 39000000
INFO @ Fri, 06 Jan 2017 14:32:05: 40000000
INFO @ Fri, 06 Jan 2017 14:32:07: 41000000
INFO @ Fri, 06 Jan 2017 14:32:09: 42000000
INFO @ Fri, 06 Jan 2017 14:32:10: 43000000
INFO @ Fri, 06 Jan 2017 14:32:12: 44000000
INFO @ Fri, 06 Jan 2017 14:32:14: 45000000
INFO @ Fri, 06 Jan 2017 14:32:15: 46000000
INFO @ Fri, 06 Jan 2017 14:32:17: 47000000
INFO @ Fri, 06 Jan 2017 14:32:19: 48000000
INFO @ Fri, 06 Jan 2017 14:32:20: 49000000
INFO @ Fri, 06 Jan 2017 14:32:22: 50000000
INFO @ Fri, 06 Jan 2017 14:32:24: #1 tag size is determined as 69 bps
INFO @ Fri, 06 Jan 2017 14:32:24: #1 tag size = 69
INFO @ Fri, 06 Jan 2017 14:32:24: #1 total tags in treatment: 2457358
INFO @ Fri, 06 Jan 2017 14:32:24: #1 total tags in control: 50000000
INFO @ Fri, 06 Jan 2017 14:32:24: #1 finished!
INFO @ Fri, 06 Jan 2017 14:32:24: #2 Build Peak Model...
INFO @ Fri, 06 Jan 2017 14:32:24: #2 Skipped...
INFO @ Fri, 06 Jan 2017 14:32:24: #2 Use 140 as fragment length
INFO @ Fri, 06 Jan 2017 14:32:24: #3 Call peaks...
INFO @ Fri, 06 Jan 2017 14:32:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Fri, 06 Jan 2017 14:32:24: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 06 Jan 2017 14:35:20: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Fri, 06 Jan 2017 14:35:20: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Fri, 06 Jan 2017 14:35:20: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Fri, 06 Jan 2017 14:35:20: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Fri, 06 Jan 2017 14:35:20: #3 Call peaks for each chromosome...
INFO @ Fri, 06 Jan 2017 14:40:04: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Fri, 06 Jan 2017 14:40:13: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Fri, 06 Jan 2017 14:40:18: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Fri, 06 Jan 2017 14:40:21: Done!
INFO @ Fri, 06 Jan 2017 14:40:27:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Fri, 06 Jan 2017 14:40:27: #1 read tag files...
INFO @ Fri, 06 Jan 2017 14:40:27: #1 read treatment tags...
INFO @ Fri, 06 Jan 2017 14:40:29: 1000000
INFO @ Fri, 06 Jan 2017 14:40:31: 2000000
INFO @ Fri, 06 Jan 2017 14:40:32: #1.2 read input tags...
INFO @ Fri, 06 Jan 2017 14:40:34: 1000000
INFO @ Fri, 06 Jan 2017 14:40:37: 2000000
INFO @ Fri, 06 Jan 2017 14:40:39: 3000000
INFO @ Fri, 06 Jan 2017 14:40:41: 4000000
INFO @ Fri, 06 Jan 2017 14:40:42: 5000000
INFO @ Fri, 06 Jan 2017 14:40:44: 6000000
INFO @ Fri, 06 Jan 2017 14:40:46: 7000000
INFO @ Fri, 06 Jan 2017 14:40:48: 8000000
INFO @ Fri, 06 Jan 2017 14:40:50: 9000000
INFO @ Fri, 06 Jan 2017 14:40:52: 10000000
INFO @ Fri, 06 Jan 2017 14:40:54: 11000000
INFO @ Fri, 06 Jan 2017 14:40:55: 12000000
INFO @ Fri, 06 Jan 2017 14:40:57: 13000000
INFO @ Fri, 06 Jan 2017 14:40:59: 14000000
INFO @ Fri, 06 Jan 2017 14:41:01: 15000000
INFO @ Fri, 06 Jan 2017 14:41:03: 16000000
INFO @ Fri, 06 Jan 2017 14:41:05: 17000000
INFO @ Fri, 06 Jan 2017 14:41:07: 18000000
INFO @ Fri, 06 Jan 2017 14:41:08: 19000000
INFO @ Fri, 06 Jan 2017 14:41:10: 20000000
INFO @ Fri, 06 Jan 2017 14:41:12: 21000000
INFO @ Fri, 06 Jan 2017 14:41:14: 22000000
INFO @ Fri, 06 Jan 2017 14:41:15: 23000000
INFO @ Fri, 06 Jan 2017 14:41:17: 24000000
INFO @ Fri, 06 Jan 2017 14:41:19: 25000000
INFO @ Fri, 06 Jan 2017 14:41:21: 26000000
INFO @ Fri, 06 Jan 2017 14:41:23: 27000000
INFO @ Fri, 06 Jan 2017 14:41:25: 28000000
INFO @ Fri, 06 Jan 2017 14:41:26: 29000000
INFO @ Fri, 06 Jan 2017 14:41:28: 30000000
INFO @ Fri, 06 Jan 2017 14:41:30: 31000000
INFO @ Fri, 06 Jan 2017 14:41:31: 32000000
INFO @ Fri, 06 Jan 2017 14:41:33: 33000000
INFO @ Fri, 06 Jan 2017 14:41:35: 34000000
INFO @ Fri, 06 Jan 2017 14:41:37: 35000000
INFO @ Fri, 06 Jan 2017 14:41:38: 36000000
INFO @ Fri, 06 Jan 2017 14:41:40: 37000000
INFO @ Fri, 06 Jan 2017 14:41:42: 38000000
INFO @ Fri, 06 Jan 2017 14:41:43: 39000000
INFO @ Fri, 06 Jan 2017 14:41:45: 40000000
INFO @ Fri, 06 Jan 2017 14:41:47: 41000000
INFO @ Fri, 06 Jan 2017 14:41:49: 42000000
INFO @ Fri, 06 Jan 2017 14:41:50: 43000000
INFO @ Fri, 06 Jan 2017 14:41:52: 44000000
INFO @ Fri, 06 Jan 2017 14:41:54: 45000000
INFO @ Fri, 06 Jan 2017 14:41:55: 46000000
INFO @ Fri, 06 Jan 2017 14:41:57: 47000000
INFO @ Fri, 06 Jan 2017 14:41:59: 48000000
INFO @ Fri, 06 Jan 2017 14:42:01: 49000000
INFO @ Fri, 06 Jan 2017 14:42:02: 50000000
INFO @ Fri, 06 Jan 2017 14:42:04: #1 tag size is determined as 69 bps
INFO @ Fri, 06 Jan 2017 14:42:04: #1 tag size = 69
INFO @ Fri, 06 Jan 2017 14:42:04: #1 total tags in treatment: 2457358
INFO @ Fri, 06 Jan 2017 14:42:04: #1 total tags in control: 50000000
INFO @ Fri, 06 Jan 2017 14:42:04: #1 finished!
INFO @ Fri, 06 Jan 2017 14:42:04: #2 Build Peak Model...
INFO @ Fri, 06 Jan 2017 14:42:04: #2 Skipped...
INFO @ Fri, 06 Jan 2017 14:42:04: #2 Use 140 as fragment length
INFO @ Fri, 06 Jan 2017 14:42:04: #3 Call peaks...
INFO @ Fri, 06 Jan 2017 14:42:04: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Fri, 06 Jan 2017 14:42:04: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 06 Jan 2017 14:44:53: #3 Call peaks for each chromosome...
INFO @ Fri, 06 Jan 2017 14:47:52: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Fri, 06 Jan 2017 14:48:02: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Fri, 06 Jan 2017 14:48:09: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Fri, 06 Jan 2017 14:48:19: Done!
|
| Num | 4 | | ID | task.callpeak_macs2.macs2_rep1_pr2.line_71.id_13 | | Name | macs2 rep1-pr2 | | Thread | thread_Root | | PID | 24245 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-06 14:30:37 | | End | 2017-01-06 14:48:51 | | Elapsed | 00:18:13 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
29433 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Fri, 06 Jan 2017 14:30:54:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 140 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Fri, 06 Jan 2017 14:30:54: #1 read tag files...
INFO @ Fri, 06 Jan 2017 14:30:54: #1 read treatment tags...
INFO @ Fri, 06 Jan 2017 14:30:56: 1000000
INFO @ Fri, 06 Jan 2017 14:30:57: 2000000
INFO @ Fri, 06 Jan 2017 14:30:58: #1.2 read input tags...
INFO @ Fri, 06 Jan 2017 14:31:00: 1000000
INFO @ Fri, 06 Jan 2017 14:31:02: 2000000
INFO @ Fri, 06 Jan 2017 14:31:03: 3000000
INFO @ Fri, 06 Jan 2017 14:31:05: 4000000
INFO @ Fri, 06 Jan 2017 14:31:06: 5000000
INFO @ Fri, 06 Jan 2017 14:31:08: 6000000
INFO @ Fri, 06 Jan 2017 14:31:09: 7000000
INFO @ Fri, 06 Jan 2017 14:31:11: 8000000
INFO @ Fri, 06 Jan 2017 14:31:12: 9000000
INFO @ Fri, 06 Jan 2017 14:31:14: 10000000
INFO @ Fri, 06 Jan 2017 14:31:15: 11000000
INFO @ Fri, 06 Jan 2017 14:31:17: 12000000
INFO @ Fri, 06 Jan 2017 14:31:18: 13000000
INFO @ Fri, 06 Jan 2017 14:31:20: 14000000
INFO @ Fri, 06 Jan 2017 14:31:22: 15000000
INFO @ Fri, 06 Jan 2017 14:31:23: 16000000
INFO @ Fri, 06 Jan 2017 14:31:25: 17000000
INFO @ Fri, 06 Jan 2017 14:31:26: 18000000
INFO @ Fri, 06 Jan 2017 14:31:28: 19000000
INFO @ Fri, 06 Jan 2017 14:31:29: 20000000
INFO @ Fri, 06 Jan 2017 14:31:31: 21000000
INFO @ Fri, 06 Jan 2017 14:31:32: 22000000
INFO @ Fri, 06 Jan 2017 14:31:34: 23000000
INFO @ Fri, 06 Jan 2017 14:31:35: 24000000
INFO @ Fri, 06 Jan 2017 14:31:37: 25000000
INFO @ Fri, 06 Jan 2017 14:31:39: 26000000
INFO @ Fri, 06 Jan 2017 14:31:40: 27000000
INFO @ Fri, 06 Jan 2017 14:31:42: 28000000
INFO @ Fri, 06 Jan 2017 14:31:43: 29000000
INFO @ Fri, 06 Jan 2017 14:31:45: 30000000
INFO @ Fri, 06 Jan 2017 14:31:46: 31000000
INFO @ Fri, 06 Jan 2017 14:31:48: 32000000
INFO @ Fri, 06 Jan 2017 14:31:49: 33000000
INFO @ Fri, 06 Jan 2017 14:31:51: 34000000
INFO @ Fri, 06 Jan 2017 14:31:52: 35000000
INFO @ Fri, 06 Jan 2017 14:31:54: 36000000
INFO @ Fri, 06 Jan 2017 14:31:55: 37000000
INFO @ Fri, 06 Jan 2017 14:31:57: 38000000
INFO @ Fri, 06 Jan 2017 14:31:59: 39000000
INFO @ Fri, 06 Jan 2017 14:32:00: 40000000
INFO @ Fri, 06 Jan 2017 14:32:02: 41000000
INFO @ Fri, 06 Jan 2017 14:32:04: 42000000
INFO @ Fri, 06 Jan 2017 14:32:05: 43000000
INFO @ Fri, 06 Jan 2017 14:32:07: 44000000
INFO @ Fri, 06 Jan 2017 14:32:09: 45000000
INFO @ Fri, 06 Jan 2017 14:32:10: 46000000
INFO @ Fri, 06 Jan 2017 14:32:12: 47000000
INFO @ Fri, 06 Jan 2017 14:32:13: 48000000
INFO @ Fri, 06 Jan 2017 14:32:15: 49000000
INFO @ Fri, 06 Jan 2017 14:32:17: 50000000
INFO @ Fri, 06 Jan 2017 14:32:18: #1 tag size is determined as 69 bps
INFO @ Fri, 06 Jan 2017 14:32:18: #1 tag size = 69
INFO @ Fri, 06 Jan 2017 14:32:18: #1 total tags in treatment: 2457358
INFO @ Fri, 06 Jan 2017 14:32:18: #1 total tags in control: 50000000
INFO @ Fri, 06 Jan 2017 14:32:18: #1 finished!
INFO @ Fri, 06 Jan 2017 14:32:18: #2 Build Peak Model...
INFO @ Fri, 06 Jan 2017 14:32:18: #2 Skipped...
INFO @ Fri, 06 Jan 2017 14:32:18: #2 Use 140 as fragment length
INFO @ Fri, 06 Jan 2017 14:32:18: #3 Call peaks...
INFO @ Fri, 06 Jan 2017 14:32:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Fri, 06 Jan 2017 14:32:18: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 06 Jan 2017 14:36:20: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Fri, 06 Jan 2017 14:36:20: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg
INFO @ Fri, 06 Jan 2017 14:36:20: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg
INFO @ Fri, 06 Jan 2017 14:36:20: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Fri, 06 Jan 2017 14:36:20: #3 Call peaks for each chromosome...
INFO @ Fri, 06 Jan 2017 14:41:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Fri, 06 Jan 2017 14:41:11: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak
INFO @ Fri, 06 Jan 2017 14:41:15: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed
INFO @ Fri, 06 Jan 2017 14:41:18: Done!
INFO @ Fri, 06 Jan 2017 14:41:25:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 140 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/align/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Fri, 06 Jan 2017 14:41:25: #1 read tag files...
INFO @ Fri, 06 Jan 2017 14:41:25: #1 read treatment tags...
INFO @ Fri, 06 Jan 2017 14:41:27: 1000000
INFO @ Fri, 06 Jan 2017 14:41:29: 2000000
INFO @ Fri, 06 Jan 2017 14:41:30: #1.2 read input tags...
INFO @ Fri, 06 Jan 2017 14:41:31: 1000000
INFO @ Fri, 06 Jan 2017 14:41:33: 2000000
INFO @ Fri, 06 Jan 2017 14:41:34: 3000000
INFO @ Fri, 06 Jan 2017 14:41:36: 4000000
INFO @ Fri, 06 Jan 2017 14:41:37: 5000000
INFO @ Fri, 06 Jan 2017 14:41:39: 6000000
INFO @ Fri, 06 Jan 2017 14:41:40: 7000000
INFO @ Fri, 06 Jan 2017 14:41:42: 8000000
INFO @ Fri, 06 Jan 2017 14:41:43: 9000000
INFO @ Fri, 06 Jan 2017 14:41:45: 10000000
INFO @ Fri, 06 Jan 2017 14:41:46: 11000000
INFO @ Fri, 06 Jan 2017 14:41:48: 12000000
INFO @ Fri, 06 Jan 2017 14:41:49: 13000000
INFO @ Fri, 06 Jan 2017 14:41:51: 14000000
INFO @ Fri, 06 Jan 2017 14:41:53: 15000000
INFO @ Fri, 06 Jan 2017 14:41:54: 16000000
INFO @ Fri, 06 Jan 2017 14:41:56: 17000000
INFO @ Fri, 06 Jan 2017 14:41:57: 18000000
INFO @ Fri, 06 Jan 2017 14:41:59: 19000000
INFO @ Fri, 06 Jan 2017 14:42:00: 20000000
INFO @ Fri, 06 Jan 2017 14:42:02: 21000000
INFO @ Fri, 06 Jan 2017 14:42:04: 22000000
INFO @ Fri, 06 Jan 2017 14:42:05: 23000000
INFO @ Fri, 06 Jan 2017 14:42:07: 24000000
INFO @ Fri, 06 Jan 2017 14:42:08: 25000000
INFO @ Fri, 06 Jan 2017 14:42:10: 26000000
INFO @ Fri, 06 Jan 2017 14:42:11: 27000000
INFO @ Fri, 06 Jan 2017 14:42:13: 28000000
INFO @ Fri, 06 Jan 2017 14:42:14: 29000000
INFO @ Fri, 06 Jan 2017 14:42:16: 30000000
INFO @ Fri, 06 Jan 2017 14:42:17: 31000000
INFO @ Fri, 06 Jan 2017 14:42:19: 32000000
INFO @ Fri, 06 Jan 2017 14:42:20: 33000000
INFO @ Fri, 06 Jan 2017 14:42:22: 34000000
INFO @ Fri, 06 Jan 2017 14:42:23: 35000000
INFO @ Fri, 06 Jan 2017 14:42:25: 36000000
INFO @ Fri, 06 Jan 2017 14:42:27: 37000000
INFO @ Fri, 06 Jan 2017 14:42:28: 38000000
INFO @ Fri, 06 Jan 2017 14:42:30: 39000000
INFO @ Fri, 06 Jan 2017 14:42:31: 40000000
INFO @ Fri, 06 Jan 2017 14:42:33: 41000000
INFO @ Fri, 06 Jan 2017 14:42:34: 42000000
INFO @ Fri, 06 Jan 2017 14:42:36: 43000000
INFO @ Fri, 06 Jan 2017 14:42:37: 44000000
INFO @ Fri, 06 Jan 2017 14:42:39: 45000000
INFO @ Fri, 06 Jan 2017 14:42:40: 46000000
INFO @ Fri, 06 Jan 2017 14:42:42: 47000000
INFO @ Fri, 06 Jan 2017 14:42:43: 48000000
INFO @ Fri, 06 Jan 2017 14:42:45: 49000000
INFO @ Fri, 06 Jan 2017 14:42:46: 50000000
INFO @ Fri, 06 Jan 2017 14:42:48: #1 tag size is determined as 69 bps
INFO @ Fri, 06 Jan 2017 14:42:48: #1 tag size = 69
INFO @ Fri, 06 Jan 2017 14:42:48: #1 total tags in treatment: 2457358
INFO @ Fri, 06 Jan 2017 14:42:48: #1 total tags in control: 50000000
INFO @ Fri, 06 Jan 2017 14:42:48: #1 finished!
INFO @ Fri, 06 Jan 2017 14:42:48: #2 Build Peak Model...
INFO @ Fri, 06 Jan 2017 14:42:48: #2 Skipped...
INFO @ Fri, 06 Jan 2017 14:42:48: #2 Use 140 as fragment length
INFO @ Fri, 06 Jan 2017 14:42:48: #3 Call peaks...
INFO @ Fri, 06 Jan 2017 14:42:48: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Fri, 06 Jan 2017 14:42:48: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 06 Jan 2017 14:45:19: #3 Call peaks for each chromosome...
INFO @ Fri, 06 Jan 2017 14:48:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls
INFO @ Fri, 06 Jan 2017 14:48:19: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak
INFO @ Fri, 06 Jan 2017 14:48:25: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak
INFO @ Fri, 06 Jan 2017 14:48:30: Done!
|
| Num | 5 | | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_14 | | Name | naive_overlap_thresh | | Thread | thread_Root | | PID | 24363 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-07 02:16:30 | | End | 2017-01-07 02:17:52 | | Elapsed | 00:01:21 | | Timeout | 01:00:00 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
| | Dependencies | | |
# SYS command. line 61
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 64
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | \
intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz
# SYS command. line 72
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[dXY]+[ ]' | awk 'BEGIN{OFS=" "} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
# SYS command. line 74
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz
# SYS command. line 76
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
22346 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270466.1 949 1125 . 0 . 18.0989862151145 -1 3.27475805435201 88
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270466.1 949 1125 . 0 . 18.0989862151145 -1 3.27475805435201 88
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1 2570 2746 . 0 . 15.5184946770447 -1 3.57050402286212 88
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1 2570 2746 . 0 . 15.5184946770447 -1 3.57050402286212 88
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000225.1 131664 131840 . 0 . 6.99332982853515 -1 4.96087491617322 88
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/overlap/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000225.1 131664 131840 . 0 . 6.99332982853515 -1 4.96087491617322 88
|
| Num | 6 | | ID | task.callpeak_idr.idr2_rep1_pr.line_73.id_15 | | Name | idr2 rep1-pr | | Thread | thread_Root | | PID | 24364 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2017-01-07 02:17:53 | | End | 2017-01-07 02:17:53 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.12-col.bed.gz
| | Dependencies | | |
# SYS command. line 75
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 77
idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370898_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370898_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/spp/rep1/SRR1370898_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
--plot --use-best-multisummit-IDR
# SYS command. line 81
idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 84
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.13-col.bed.gz
# SYS command. line 87
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.narrowPeak.gz
# SYS command. line 88
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.12-col.bed.gz
# SYS command. line 90
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[dXY]+[ ]' | awk 'BEGIN{OFS=" "} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 91
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS=" "} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.narrowPeak.gz
# SYS command. line 92
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS=" "} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.12-col.bed.gz
# SYS command. line 94
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.unthresholded-peaks.txt
# SYS command. line 95
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/out/peak/idr/pseudo_reps/rep1/ZNF16_rep1-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 97
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
22455 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [0.75 1.20 0.86 0.51]
Number of reported peaks - 1231/1231 (100.0%)
Number of peaks passing IDR cutoff of 0.05 - 200/1231 (16.2%)
--------------------Post mortem info--------------------
==============================================================
job_number: 24364
submission_time: Sat Jan 7 02:17:53 2017
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/software/sratoolkit/2.5.2/bin/:/software/ascp/:/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/Najafabadi2015Data/hg38Mapping/ZNF16
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/chipseq.bds.20170106_143022_973/task.callpeak_idr.idr2_rep1_pr.line_73.id_15.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF16/chipseq.bds.20170106_143022_973/task.callpeak_idr.idr2_rep1_pr.line_73.id_15.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 43899 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/0,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/ascp/3.5.6:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/homer/default,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=1080,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=/software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/software/sratoolkit/2.5.2/bin/:/software/ascp/:/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:10.0,SGE_CELL=default,STY=33307.ZNF16.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_veRoBQ,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/Najafabadi2015Data/hg38Mapping/ZNF16,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:ascp/3.5.6:sratoolkit/2.5.2:homer/default,SSH_CONNECTION=171.65.77.8 43899 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,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
scheduling info: queue instance "q@kali" dropped because it is temporarily not available
queue instance "q@surya" dropped because it is disabled
|