Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
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Program ID | chipseq.bds.20161205_182001_593 |
Start time | 2016-12-05 18:20:01 |
Run time | 29 days 20:41:50.780 |
Tasks executed | 3 |
Tasks failed | 1 |
Tasks failed names | spp rep1 |
Arguments* | [-title, ZIC2, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZIC2/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/align/rep1/SRR1370909_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $] |
System* | sge |
Cpus* | -1 |
Exit value | 1 |
Thread ID | Parent | Tasks |
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thread_Root | None | chipseq.bds.20161205_182001_593/task.callpeak_spp.spp_rep1.line_54.id_10 chipseq.bds.20161205_182001_593/task.callpeak_spp.spp_rep1_pr1.line_54.id_11 chipseq.bds.20161205_182001_593/task.callpeak_spp.spp_rep1_pr2.line_54.id_12 |
thread_41 | thread_Root | |
thread_42 | thread_Root | |
Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
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| # SYS command. line 56 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 59 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 63 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/align/rep1/SRR1370909_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/ZIC2/out/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore # SYS command. line 67 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_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/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz # SYS command. line 69 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz # SYS command. line 71 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf # SYS command. line 74 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi # SYS command. line 77 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/rep1/SRR1370909_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi # SYS command. line 79 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi --------------------Error message-------------------- Task disappeared from cluster's queue. Task or node failure? | ||||||||||||||||||||||||||||||||||||||||
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| # SYS command. line 56 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 59 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 63 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/align/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.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/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore # SYS command. line 67 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.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/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz # SYS command. line 69 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz # SYS command. line 71 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf # SYS command. line 74 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi # SYS command. line 77 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi # SYS command. line 79 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi --------------------Stdout-------------------- 12397 (process ID) old priority 0, new priority 10 ################ ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/align/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.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 145 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/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1 narrowPeak output file name: NA regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak Rdata filename: NA plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign.pdf result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.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/ZIC2/out/align/pseudo_reps/rep1/pr1/SRR1370909_1.nodup.pr1.tagAlign.gz opened /tmp/17403.1.amd.q/RtmpqfE9wZ/SRR1370909_1.nodup.pr1.tagAlign30ad5c1f74a3 done. read 2073384 fragments ChIP data read length 51 [1] TRUE Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz opened /tmp/17403.1.amd.q/RtmpqfE9wZ/input15MReadsNSCLess1.05.50MSubsample.tagAlign30ad1c58bd7 done. read 50000000 fragments Control data read length 68 Calculating peak characteristics Minimum cross-correlation value 0.02966966 Minimum cross-correlation shift 1500 Top 3 cross-correlation values 0.0610632815978674 Top 3 estimates for fragment length 145 Window half size 185 Phantom peak location 55 Phantom peak Correlation 0.03443004 Normalized Strand cross-correlation coefficient (NSC) 2.058106 Relative Strand cross-correlation Coefficient (RSC) 6.594771 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= 25.48035 excluding systematic background anomalies ... done determining peaks on real data: bg.weight= 0.03924593 excluding systematic background anomalies ... done calculating statistical thresholds FDR 0.99 threshold= 2.001841 Detected 57291 peaks --------------------Stderr-------------------- Loading required package: caTools There were 50 or more warnings (use warnings() to see the first 50) | ||||||||||||||||||||||||||||||||||||||||
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| # SYS command. line 56 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 59 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 63 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/align/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.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/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore # SYS command. line 67 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.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/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz # SYS command. line 69 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz # SYS command. line 71 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf # SYS command. line 74 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi # SYS command. line 77 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi # SYS command. line 79 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi --------------------Stdout-------------------- 2621 (process ID) old priority 0, new priority 10 ################ ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/align/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.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 145 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/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2 narrowPeak output file name: NA regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak Rdata filename: NA plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign.pdf result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.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/ZIC2/out/align/pseudo_reps/rep1/pr2/SRR1370909_1.nodup.pr2.tagAlign.gz opened /tmp/17404.1.q/RtmptJ6lFs/SRR1370909_1.nodup.pr2.tagAligna7d59390286 done. read 2073383 fragments ChIP data read length 51 [1] TRUE Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz opened /tmp/17404.1.q/RtmptJ6lFs/input15MReadsNSCLess1.05.50MSubsample.tagAligna7d5ea1d910 done. read 50000000 fragments Control data read length 68 Calculating peak characteristics Minimum cross-correlation value 0.02949811 Minimum cross-correlation shift 1500 Top 3 cross-correlation values 0.0608959780731203 Top 3 estimates for fragment length 145 Window half size 185 Phantom peak location 55 Phantom peak Correlation 0.03436503 Normalized Strand cross-correlation coefficient (NSC) 2.064402 Relative Strand cross-correlation Coefficient (RSC) 6.451279 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= 25.44636 excluding systematic background anomalies ... done determining peaks on real data: bg.weight= 0.03929836 excluding systematic background anomalies ... done calculating statistical thresholds FDR 0.99 threshold= 2.001751 Detected 56977 peaks --------------------Stderr-------------------- Loading required package: caTools There were 50 or more warnings (use warnings() to see the first 50) |
Type | Name | Value |
---|---|---|
string | _ | /usr/bin/bds |
string | _LMFILES_ | /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6 |
bool | allowEmpty | false |
string[] | args | [-title, ZIC2, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZIC2/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2/out/align/rep1/SRR1370909_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $] |
string | ASCPKEY | /software/ascp/etc/asperaweb_id_dsa.openssh |
bool | canFail | false |
int | cpus | -1 |
int | cpusLocal | 56 |
int | day | 86400 |
string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
string | DERBY_HOME | /usr/lib/jvm/java-8-oracle/db |
string | DISPLAY | localhost:12.0 |
real | E | 2.718281828459045 |
string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
int | G | 1073741824 |
string | HOME | /users/imk1/ |
int | hour | 3600 |
string | J2REDIR | /usr/lib/jvm/java-8-oracle/jre |
string | J2SDKDIR | /usr/lib/jvm/java-8-oracle |
string | JAVA_HOME | /usr/lib/jvm/java-8-oracle |
int | K | 1024 |
string | KERAS_DIR | /users/imk1/.local/lib/python2.7/site-packages/keras/ |
string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_N5SeQf |
string | LANG | en_US.UTF-8 |
string | LOADEDMODULES | modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6 |
string | LOGNAME | imk1 |
int | M | 1048576 |
string | /var/mail/imk1 | |
int | mem | -1 |
int | minute | 60 |
string | MODULE_VERSION | 3.2.10 |
string | MODULE_VERSION_STACK | 3.2.10 |
string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
string | MODULESAPPSDIR | /software |
string | MODULESHOME | /software/env_module/3.2.10 |
string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
string | node | |
int | P | 1125899906842624 |
string | PATH | /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/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:/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:/software/ascp/:/software/sratoolkit/2.5.2/bin/:/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:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect |
string | PERL5LIB | /users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5 |
string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5 |
string | PERL_MB_OPT | --install_base \"/users/imk1/perl5\" |
string | PERL_MM_OPT | INSTALL_BASE=/users/imk1/perl5 |
real | PI | 3.141592653589793 |
string | ppwd | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2 |
string | programName | chipseq.bds |
string | programPath | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
string | PWD | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZIC2 |
string | PYTHONPATH | /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/ |
string | queue | |
int | retry | 0 |
string | RULEFITBASE | /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/ |
string | SHELL | /bin/bash |
string | SHLVL | 3 |
string | SSH_CLIENT | 171.65.77.8 55144 22 |
string | SSH_CONNECTION | 171.65.77.8 55144 171.65.76.63 22 |
string | SSH_TTY | /dev/pts/4 |
string | STY | 3549.ZIC2.BDS |
string | system | sge |
int | T | 1099511627776 |
string | TERM | screen |
string | TERMCAP | SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD: |
int | timeout | -1 |
string | USER | imk1 |
string | UTIL_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/ |
int | walltimeout | 8640000 |
int | week | 604800 |
string | WINDOW | 0 |
string | XDG_RUNTIME_DIR | /run/user/1048 |
string | XDG_SESSION_ID | 20 |
string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |