Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
Num | 1 | ID | task.postalign_bed.xcor_rep1.line_205.id_10 | Name | xcor rep1 | Thread | thread_41 | PID | 3427 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2016-11-03 16:52:25 | End | 2016-11-03 17:06:23 | Elapsed | 00:13:58 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.15M.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.plot.pdf
| Dependencies | | |
# SYS command. line 207
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 210
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 216
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.15M.tagAlign.gz -p=3 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.qc
# SYS command. line 219
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.qc.tmp
# SYS command. line 220
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.qc
# SYS command. line 222
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
38760 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 3
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.15M.tagAlign.gz
opened /tmp/3427.1.q/RtmpHzTf4v/SRR836478.nodup.15M.tagAlign97f241c1dd9a
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1957265
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.213570323465724,0.213561115880272,0.204152170857273
Top 3 estimates for fragment length 130,140,260
Window half size 440
Phantom peak location 55
Phantom peak Correlation 0.2063379
Normalized Strand cross-correlation coefficient (NSC) 1.091167
Relative Strand Cross correlation Coefficient (RSC) 1.68158
Phantom Peak Quality Tag 2
null device
1
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
|
Num | 2 | ID | task.callpeak_spp.spp_rep1.line_54.id_11 | Name | spp rep1 | Thread | thread_Root | PID | 3495 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-03 17:06:24 | End | 2016-11-04 08:39:58 | Elapsed | 15:33:34 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
| Dependencies | | |
# SYS command. line 56
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 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/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1 -speak=130 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 69
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
20107 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 130
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/MouseMutantData/SRR836478/out/peak/spp/rep1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/rep1/SRR836478.nodup.tagAlign.gz
opened /tmp/3495.1.q/RtmpEP3tjd/SRR836478.nodup.tagAlign4f0038f33d30
done. read 17063104 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
opened /tmp/3495.1.q/RtmpEP3tjd/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign4f0034be69f7
done. read 3384182 fragments
Control data read length 50
Calculating peak characteristics
Minimum cross-correlation value 0.2162675
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.235982783414474
Top 3 estimates for fragment length 130
Window half size 440
Phantom peak location 55
Phantom peak Correlation 0.2279869
Normalized Strand cross-correlation coefficient (NSC) 1.091162
Relative Strand Cross correlation Coefficient (RSC) 1.682272
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= 0.2037103 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 4.908933 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2
Detected 1157066 peaks
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 41 warnings (use warnings() to see them)
|
Num | 3 | ID | task.callpeak_spp.spp_rep1_pr1.line_54.id_12 | Name | spp rep1-pr1 | Thread | thread_Root | PID | 3496 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-03 17:06:26 | End | 2016-11-04 06:41:09 | Elapsed | 13:34:43 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
| Dependencies | | |
# SYS command. line 56
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 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/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1 -speak=130 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 69
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
20307 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 130
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/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign.gz
opened /tmp/3496.1.q/RtmpLBsZ6o/SRR836478.nodup.pr1.tagAlign4fdc774be4af
done. read 8531552 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
opened /tmp/3496.1.q/RtmpLBsZ6o/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign4fdc1028b66d
done. read 3384182 fragments
Control data read length 50
Calculating peak characteristics
Minimum cross-correlation value 0.1226109
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.133795189809542
Top 3 estimates for fragment length 130
Window half size 435
Phantom peak location 55
Phantom peak Correlation 0.1292341
Normalized Strand cross-correlation coefficient (NSC) 1.091218
Relative Strand Cross correlation Coefficient (RSC) 1.688639
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= 0.4056811 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 2.46499 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 12.24185
Detected 4325 peaks
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 34 warnings (use warnings() to see them)
|
Num | 4 | ID | task.callpeak_spp.spp_rep1_pr2.line_54.id_13 | Name | spp rep1-pr2 | Thread | thread_Root | PID | 3497 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-03 17:06:27 | End | 2016-11-04 06:54:22 | Elapsed | 13:47:55 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
| Dependencies | | |
# SYS command. line 56
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 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/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2 -speak=130 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 69
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
20306 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 130
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/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign.gz
opened /tmp/3497.1.q/RtmpwAP9to/SRR836478.nodup.pr2.tagAlign4fc74f85852e
done. read 8531552 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
opened /tmp/3497.1.q/RtmpwAP9to/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign4fc73194fc00
done. read 3384182 fragments
Control data read length 50
Calculating peak characteristics
Minimum cross-correlation value 0.1229755
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.134267836480185
Top 3 estimates for fragment length 130
Window half size 440
Phantom peak location 55
Phantom peak Correlation 0.1296902
Normalized Strand cross-correlation coefficient (NSC) 1.091826
Relative Strand Cross correlation Coefficient (RSC) 1.681735
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= 0.405739 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 2.464639 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 11.69902
Detected 5072 peaks
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
|
Num | 5 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_32.id_14 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 3760 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 08:40:00 | End | 2016-11-04 08:41:13 | Elapsed | 00:01:13 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
| Dependencies | | |
# SYS command. line 34
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 37
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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 -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.PooledInRep1AndRep2.regionPeak.gz
# SYS command. line 43
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
# SYS command. line 45
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.PooledInRep1AndRep2.regionPeak.gz
# SYS command. line 47
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
19321 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL456359.1 19374 19810 . 0 . 40.2783616100353 -1 0.568891628074813 218
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL456359.1 19374 19810 . 0 . 40.2783616100353 -1 0.568891628074813 218
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL456359.1 19384 19824 . 0 . 33.1118463877834 -1 0.495703532237389 220
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL456359.1 19384 19824 . 0 . 33.1118463877834 -1 0.495703532237389 220
|
Num | 6 | ID | task.callpeak_idr.idr2_rep1_pr.line_70.id_15 | Name | idr2 rep1-pr | Thread | thread_Root | PID | 3762 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 08:41:14 | End | 2016-11-04 08:42:28 | Elapsed | 00:01:13 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.gz
| Dependencies | | |
# SYS command. line 72
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr1/SRR836478.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/pseudo_reps/rep1/pr2/SRR836478.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/spp/rep1/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
--plot --use-best-multisummit-IDR
# SYS command. line 78
idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 81
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/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.13-col.bed.gz
# SYS command. line 84
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.narrowPeak.gz
# SYS command. line 85
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.gz
# SYS command. line 87
echo
# SYS command. line 88
echo
# SYS command. line 89
echo
# SYS command. line 91
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.unthresholded-peaks.txt
# SYS command. line 92
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 94
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
45168 (process ID) old priority 0, new priority 10
Waiting for 47 seconds.
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.25 1.19 0.76 0.23]
Number of reported peaks - 3176/3176 (100.0%)
Number of peaks passing IDR cutoff of 0.05 - 242/3176 (7.6%)
|
Num | 7 | ID | task.callpeak_idr.idr_final_qc.line_205.id_18 | Name | idr final qc | Thread | thread_Root | PID | 3763 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 08:42:29 | End | 2016-11-04 08:43:43 | Elapsed | 00:01:13 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/SRR836478_IDR_final.qc
| Dependencies | | |
# SYS command. line 207
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 209
echo -e "Nt\tN1 ""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/SRR836478_IDR_final.qc
# SYS command. line 210
echo -e "0\t241 ""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/SRR836478_IDR_final.qc
# SYS command. line 212
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
26163 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
|
Num | 8 | ID | task.report.peak2hammock.line_357.id_19 | Name | peak2hammock | Thread | thread_Root | PID | 45783 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 08:43:43 | End | 2016-11-04 08:43:45 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.hammock.gz
| Dependencies | | |
# SYS command. line 359
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 360
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp
# SYS command. line 362
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.hammock
# SYS command. line 363
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/SPP/overlap/SRR836478.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp
--------------------Stdout--------------------
45788 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
|
Num | 9 | ID | task.report.peak2hammock.line_357.id_20 | Name | peak2hammock | Thread | thread_Root | PID | 45873 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 08:43:46 | End | 2016-11-04 08:43:47 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.hammock.gz
| Dependencies | | |
# SYS command. line 359
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 360
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.tmp
# SYS command. line 362
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.hammock
# SYS command. line 363
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/peak/idr/pseudo_reps/rep1/SRR836478_rep1-pr.IDR0.05.12-col.bed.tmp
--------------------Stdout--------------------
45877 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
|
Num | 10 | ID | task.graphviz.report.line_97.id_21 | Name | report | Thread | thread_Root | PID | 46052 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 08:43:48 | End | 2016-11-04 08:43:49 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | | Output files | | Dependencies | | |
# SYS command. line 98
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/report/SRR836478_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/report/SRR836478_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/report/SRR836478_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout--------------------
46058 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
|
Num | 11 | ID | task.report.pdf2png.line_324.id_26 | Name | pdf2png | Thread | thread_Root | PID | 46057 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 08:43:48 | End | 2016-11-04 08:43:49 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.plot.pdf
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.plot.png
| Dependencies | | |
# SYS command. line 325
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 326
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836478/out/qc/rep1/SRR836478.nodup.15M.cc.plot.pdf
--------------------Stdout--------------------
46067 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
|