BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161118_165934_055
Start time 2016-11-18 16:59:34
Run time 6 days 20:38:11.502
Tasks executed 3
Tasks failed 1
Tasks failed names 
spp rep1
Arguments* [-title, MZF1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/MZF1/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_1.bam, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, idr, $]
System* sge
Cpus* -1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None 
 chipseq.bds.20161118_165934_055/task.callpeak_spp.spp_rep1.line_54.id_10
chipseq.bds.20161118_165934_055/task.callpeak_spp.spp_rep1_pr1.line_54.id_11
chipseq.bds.20161118_165934_055/task.callpeak_spp.spp_rep1_pr2.line_54.id_12
thread_41 thread_Root
thread_42 thread_Root

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.callpeak_spp.spp_rep1.line_54.id_10
Name spp rep1
Thread thread_Root
PID 14026
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2016-11-18 16:59:42
End 2016-11-18 16:59:42
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies 
 
# SYS command. line 56

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 59

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_VS_ss_50M_2000_GRCh38.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/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.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
 
 
--------------------Error message--------------------
Task disappeared from cluster's queue. Task or node failure?
  
--------------------Stdout--------------------
33645 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz 
opened /tmp/14026.1.amd.q/Rtmp05zAKn/SRR1370902_1.nodup.tagAlign840e188be006
done. read 18853429 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/14026.1.amd.q/Rtmp05zAKn/ss_50M_2000_GRCh38.nodup.tagAlign840e7ce580f8
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.2089171 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.223033206130548 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.2141388 
Normalized Strand cross-correlation coefficient (NSC) 1.067568 
Relative Strand cross-correlation Coefficient (RSC) 2.703333 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3
Num 2
ID task.callpeak_spp.spp_rep1_pr1.line_54.id_11
Name spp rep1-pr1
Thread thread_Root
PID 14027
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-18 16:59:43
End 2016-11-19 10:22:43
Elapsed 17:23:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies 
 
# SYS command. line 56

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 59

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_VS_ss_50M_2000_GRCh38.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/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
33788 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.gz 
opened /tmp/14027.1.amd.q/RtmpNyjiAn/SRR1370902_1.nodup.pr1.tagAlign846758a5f31f
done. read 9426715 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/14027.1.amd.q/RtmpNyjiAn/ss_50M_2000_GRCh38.nodup.tagAlign8467463694f2
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.117472 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.125343112019051 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.1204181 
Normalized Strand cross-correlation coefficient (NSC) 1.067004 
Relative Strand cross-correlation Coefficient (RSC) 2.671743 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 10.55559  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.09473656  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000075 
Detected 227875 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3
Num 3
ID task.callpeak_spp.spp_rep1_pr2.line_54.id_12
Name spp rep1-pr2
Thread thread_Root
PID 14028
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-18 16:59:44
End 2016-11-19 10:24:45
Elapsed 17:25:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies 
 
# SYS command. line 56

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 59

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_VS_ss_50M_2000_GRCh38.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/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
33939 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.gz 
opened /tmp/14028.1.amd.q/Rtmpu1Yhsd/SRR1370902_1.nodup.pr2.tagAlign84ec2346693b
done. read 9426714 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/14028.1.amd.q/Rtmpu1Yhsd/ss_50M_2000_GRCh38.nodup.tagAlign84ec26827c48
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.1172777 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.12529881447101 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.1202717 
Normalized Strand cross-correlation coefficient (NSC) 1.068394 
Relative Strand cross-correlation Coefficient (RSC) 2.679067 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 10.55458  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.09474564  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00017 
Detected 227733 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
string _LMFILES_ /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6
bool allowEmpty false
string[] args [-title, MZF1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/MZF1/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_1.bam, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, idr, $]
string ASCPKEY /software/ascp/etc/asperaweb_id_dsa.openssh
bool canFail false
int cpus -1
int cpusLocal 56
int day 86400
string DEEPLIFT_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:12.0
real E 2.718281828459045
string ENHANCER_SCRIPTS_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KERAS_DIR /users/imk1/.local/lib/python2.7/site-packages/keras/
string KRB5CCNAME FILE:/tmp/krb5cc_1048_N5SeQf
string LANG en_US.UTF-8
string LOADEDMODULES modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string MODULESAPPSDIR /software
string MODULESHOME /software/env_module/3.2.10
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string node
int P 1125899906842624
string PATH /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect
string PERL5LIB /users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5
string PERL_LOCAL_LIB_ROOT /users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5
string PERL_MB_OPT --install_base \"/users/imk1/perl5\"
string PERL_MM_OPT INSTALL_BASE=/users/imk1/perl5
real PI 3.141592653589793
string ppwd /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1
string programName chipseq.bds
string programPath /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string PWD /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1
string PYTHONPATH /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string queue
int retry 0
string RULEFITBASE /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string SHELL /bin/bash
string SHLVL 3
string SSH_CLIENT 171.65.77.8 55144 22
string SSH_CONNECTION 171.65.77.8 55144 171.65.76.63 22
string SSH_TTY /dev/pts/4
string STY 21934.MZF1.2015.BDS
string system sge
int T 1099511627776
string TERM screen
string TERMCAP SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int timeout -1
string USER imk1
string UTIL_SCRIPTS_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int walltimeout 8640000
int week 604800
string WINDOW 0
string XDG_RUNTIME_DIR /run/user/1048
string XDG_SESSION_ID 20
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt