Num | 1 | ID | task.callpeak_idr.idr2_rep1_pr.line_73.id_10 | Name | idr2 rep1-pr | Thread | thread_Root | PID | 25049 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-09 14:50:21 | End | 2017-01-09 14:54:36 | Elapsed | 00:04:15 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/spp/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_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/ZNF189/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/spp/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_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/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.13-col.bed.gz
# SYS command. line 87
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_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/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.narrowPeak.gz
# SYS command. line 88
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_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/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.12-col.bed.gz
# SYS command. line 90
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 91
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.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/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.narrowPeak.gz
# SYS command. line 92
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.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/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.gz
# SYS command. line 94
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.unthresholded-peaks.txt
# SYS command. line 95
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_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--------------------
26052 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.38 1.27 0.84 0.34]
Number of reported peaks - 72843/72843 (100.0%)
Number of peaks passing IDR cutoff of 0.05 - 11705/72843 (16.1%)
|
Num | 2 | ID | task.callpeak_idr.idr_final_qc.line_219.id_13 | Name | idr final qc | Thread | thread_Root | PID | 25147 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-09 14:54:37 | End | 2017-01-09 14:56:25 | Elapsed | 00:01:48 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/qc/ZNF189_IDR_final.qc
| Dependencies | | |
# SYS command. line 221
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 223
echo -e "Nt\tN1 N2 ""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/qc/ZNF189_IDR_final.qc
# SYS command. line 224
echo -e "0\t11667 0 ""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/qc/ZNF189_IDR_final.qc
# SYS command. line 226
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
36401 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.
|
Num | 3 | ID | task.report.peak2hammock.line_412.id_14 | Name | peak2hammock | Thread | thread_Root | PID | 49325 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-09 14:56:28 | End | 2017-01-09 14:56:37 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
| Dependencies | | |
# SYS command. line 414
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 415
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.tmp
# SYS command. line 417
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.hammock
# SYS command. line 418
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/idr/pseudo_reps/rep1/ZNF189_rep1-pr.IDR0.05.filt.12-col.bed.tmp
--------------------Stdout--------------------
49329 (process ID) old priority 0, new priority 10
|
Num | 4 | ID | task.graphviz.report.line_97.id_15 | Name | report | Thread | thread_Root | PID | 51069 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-09 14:56:38 | End | 2017-01-09 14:56:46 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | | Output files | | Dependencies | | |
# SYS command. line 98
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 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/report/ZNF189_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/report/ZNF189_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/report/ZNF189_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout--------------------
51073 (process ID) old priority 0, new priority 10
|