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_42 | PID | 3409 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2016-11-03 16:52:23 | End | 2016-11-03 17:01:46 | Elapsed | 00:09:23 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/rep1/SRR836457.nodup.15M.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.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/SRR836457/out/align/rep1/SRR836457.nodup.15M.tagAlign.gz -p=3 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.qc
# SYS command. line 219
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.qc.tmp
# SYS command. line 220
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.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--------------------
43285 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/rep1/SRR836457.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/SRR836457/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/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/rep1/SRR836457.nodup.15M.tagAlign.gz
opened /tmp/3409.1.q/RtmpH2mdvH/SRR836457.nodup.15M.tagAlignaa5b789534c8
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1936416
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.251263401709105
Top 3 estimates for fragment length 115
Window half size 350
Phantom peak location 55
Phantom peak Correlation 0.2388563
Normalized Strand cross-correlation coefficient (NSC) 1.297569
Relative Strand Cross correlation Coefficient (RSC) 1.274403
Phantom Peak Quality Tag 1
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 | 3475 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-03 17:01:47 | End | 2016-11-04 03:09:10 | Elapsed | 10:07:22 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/rep1/SRR836457.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.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/SRR836457/out/align/rep1/SRR836457.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1 -speak=115 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.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/SRR836457/out/peak/spp/rep1/SRR836457.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/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
18443 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/rep1/SRR836457.nodup.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 115
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/SRR836457/out/peak/spp/rep1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.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/SRR836457/out/align/rep1/SRR836457.nodup.tagAlign.gz
opened /tmp/3475.1.q/Rtmpc3wVS5/SRR836457.nodup.tagAlign48b372df7c91
done. read 15226445 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
opened /tmp/3475.1.q/Rtmpc3wVS5/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign48b32515de06
done. read 3384182 fragments
Control data read length 50
Calculating peak characteristics
Minimum cross-correlation value 0.1959413
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.254174013561898
Top 3 estimates for fragment length 115
Window half size 350
Phantom peak location 55
Phantom peak Correlation 0.2416746
Normalized Strand cross-correlation coefficient (NSC) 1.297195
Relative Strand Cross correlation Coefficient (RSC) 1.27331
Phantom Peak Quality Tag 1
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= 0.2510493 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 3.983281 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000011
Detected 812922 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 | 3476 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-03 17:01:48 | End | 2016-11-04 02:00:37 | Elapsed | 08:58:49 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/align/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1 -speak=115 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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--------------------
18444 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 115
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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/align/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign.gz
opened /tmp/3476.1.q/Rtmp2HL7fc/SRR836457.nodup.pr1.tagAlign48df17cb097f
done. read 7613223 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
opened /tmp/3476.1.q/Rtmp2HL7fc/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign48df78608917
done. read 3384182 fragments
Control data read length 50
Calculating peak characteristics
Minimum cross-correlation value 0.1125013
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.14600284510327
Top 3 estimates for fragment length 115
Window half size 350
Phantom peak location 55
Phantom peak Correlation 0.1388346
Normalized Strand cross-correlation coefficient (NSC) 1.297788
Relative Strand Cross correlation Coefficient (RSC) 1.272212
Phantom Peak Quality Tag 1
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= 0.4949006 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 2.020608 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 6.249786
Detected 40221 peaks
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 30 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 | 3479 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-03 17:01:49 | End | 2016-11-04 03:11:35 | Elapsed | 10:09:45 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.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/SRR836457/out/align/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2 -speak=115 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
19892 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 115
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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.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/SRR836457/out/align/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign.gz
opened /tmp/3479.1.q/RtmpmpTGka/SRR836457.nodup.pr2.tagAlign4e345725dd5b
done. read 7613222 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
opened /tmp/3479.1.q/RtmpmpTGka/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign4e3427255cc5
done. read 3384182 fragments
Control data read length 50
Calculating peak characteristics
Minimum cross-correlation value 0.1127529
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.146342391856393
Top 3 estimates for fragment length 115
Window half size 350
Phantom peak location 55
Phantom peak Correlation 0.1392458
Normalized Strand cross-correlation coefficient (NSC) 1.297904
Relative Strand Cross correlation Coefficient (RSC) 1.267868
Phantom Peak Quality Tag 1
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= 0.4946221 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 2.021746 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 6.253434
Detected 40293 peaks
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 46 warnings (use warnings() to see them)
|
Num | 5 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_32.id_14 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 3639 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 03:11:36 | End | 2016-11-04 03:46:43 | Elapsed | 00:35:06 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/SPP/overlap/SRR836457.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/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.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/SRR836457/out/peak/SPP/overlap/SRR836457.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/SRR836457/out/peak/SPP/overlap/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/SPP/overlap/SRR836457.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/SRR836457/out/peak/SPP/overlap/SRR836457.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--------------------
6251 (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 19417 19767 . 0 . 36.0757146173779 -1 1.87943205902095 175
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL456359.1 19417 19767 . 0 . 36.0757146173779 -1 1.87943205902095 175
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL456359.1 19436 19786 . 0 . 31.5603944559819 -1 1.9294189257144 175
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL456359.1 19436 19786 . 0 . 31.5603944559819 -1 1.9294189257144 175
|
Num | 6 | ID | task.callpeak_idr.idr2_rep1_pr.line_70.id_15 | Name | idr2 rep1-pr | Thread | thread_Root | PID | 3653 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 03:46:44 | End | 2016-11-04 03:59:57 | Elapsed | 00:13:13 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_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/SRR836457/out/peak/spp/pseudo_reps/rep1/pr1/SRR836457.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/pseudo_reps/rep1/pr2/SRR836457.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/spp/rep1/SRR836457.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/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_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/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.13-col.bed.gz
# SYS command. line 84
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_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/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.narrowPeak.gz
# SYS command. line 85
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.12-col.bed.gz
# SYS command. line 87
echo
# SYS command. line 88
echo
# SYS command. line 89
echo
# SYS command. line 91
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.unthresholded-peaks.txt
# SYS command. line 92
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 94
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
32729 (process ID) old priority 0, new priority 10
Waiting for 8 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: [1.33 1.18 0.79 0.45]
Number of reported peaks - 27408/27408 (100.0%)
Number of peaks passing IDR cutoff of 0.05 - 6290/27408 (22.9%)
|
Num | 7 | ID | task.callpeak_idr.idr_final_qc.line_205.id_18 | Name | idr final qc | Thread | thread_Root | PID | 3667 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 03:59:59 | End | 2016-11-04 04:06:43 | Elapsed | 00:06:43 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/SRR836457_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/SRR836457/out/qc/SRR836457_IDR_final.qc
# SYS command. line 210
echo -e "0\t6269 ""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/SRR836457_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--------------------
15189 (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 | 15540 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 04:06:44 | End | 2016-11-04 04:06:45 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/SPP/overlap/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/SPP/overlap/SRR836457.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/SRR836457/out/peak/SPP/overlap/SRR836457.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/SRR836457/out/peak/SPP/overlap/SRR836457.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/SRR836457/out/peak/SPP/overlap/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/SPP/overlap/SRR836457.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/SRR836457/out/peak/SPP/overlap/SRR836457.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp
--------------------Stdout--------------------
15544 (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 | 15621 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 04:06:46 | End | 2016-11-04 04:06:48 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_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/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_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/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.12-col.bed.hammock
# SYS command. line 363
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/peak/idr/pseudo_reps/rep1/SRR836457_rep1-pr.IDR0.05.12-col.bed.tmp
--------------------Stdout--------------------
15625 (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 | 15726 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 04:06:49 | End | 2016-11-04 04:06:50 | 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 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/report/SRR836457_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/report/SRR836457_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/report/SRR836457_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout--------------------
15732 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
|
Num | 11 | ID | task.report.pdf2png.line_324.id_26 | Name | pdf2png | Thread | thread_Root | PID | 15731 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2016-11-04 04:06:49 | End | 2016-11-04 04:06:50 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.plot.pdf
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.plot.png
| Dependencies | | |
# SYS command. line 325
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# 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/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836457/out/qc/rep1/SRR836457.nodup.15M.cc.plot.pdf
--------------------Stdout--------------------
15742 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
|