BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170407_161950_454
Start time 2017-04-07 16:19:50
Run time 01:41:48.731
Tasks executed 15
Tasks failed 3
Tasks failed names 
pool_tag ppr1
pool_tag ppr2
pool_tag pooled_rep
Arguments* [-title, ZBTB26_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, $]
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.20170407_161950_454/task.postalign_bed.pool_tag_pooled_rep.line_436.id_22
chipseq.bds.20170407_161950_454/task.postalign_bed.pool_tag_ppr1.line_436.id_23
chipseq.bds.20170407_161950_454/task.postalign_bed.pool_tag_ppr2.line_436.id_24
thread_41 thread_Root 
 chipseq.bds.20170407_161950_454_parallel_41/task.postalign_bam.nmsrt_bam_rep1.line_495.id_10
chipseq.bds.20170407_161950_454_parallel_41/task.postalign_bam.bam_to_bedpe_rep1.line_602.id_17
chipseq.bds.20170407_161950_454_parallel_41/task.postalign_bam.bedpe_to_tag_rep1.line_640.id_18
chipseq.bds.20170407_161950_454_parallel_41/task.postalign_bed.subsample_bedpe2tag_rep1.line_115.id_19
chipseq.bds.20170407_161950_454_parallel_41/task.postalign_bed.spr_PE_rep1.line_299.id_20
chipseq.bds.20170407_161950_454_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_21
thread_42 thread_Root 
 chipseq.bds.20170407_161950_454_parallel_42/task.postalign_bam.nmsrt_bam_rep2.line_495.id_11
chipseq.bds.20170407_161950_454_parallel_42/task.postalign_bam.bam_to_bedpe_rep2.line_602.id_12
chipseq.bds.20170407_161950_454_parallel_42/task.postalign_bam.bedpe_to_tag_rep2.line_640.id_13
chipseq.bds.20170407_161950_454_parallel_42/task.postalign_bed.subsample_bedpe2tag_rep2.line_115.id_14
chipseq.bds.20170407_161950_454_parallel_42/task.postalign_bed.spr_PE_rep2.line_299.id_15
chipseq.bds.20170407_161950_454_parallel_42/task.postalign_bed.xcor_rep2.line_212.id_16
thread_43 thread_Root

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.postalign_bam.nmsrt_bam_rep1.line_495.id_10
Name nmsrt_bam rep1
Thread thread_41
PID 46352
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 16:19:53
End 2017-04-07 17:27:12
Elapsed 01:07:18
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.nmsrt.bam
Dependencies 
 
# SYS command. line 497

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 500

 sambamba sort -t 1 -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.nmsrt.bam

# SYS command. line 502

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
27196 (process ID) old priority 0, new priority 19
Num 2
ID task.postalign_bam.nmsrt_bam_rep2.line_495.id_11
Name nmsrt_bam rep2
Thread thread_42
PID 46353
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 16:19:53
End 2017-04-07 17:02:59
Elapsed 00:43:05
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.nmsrt.bam
Dependencies 
 
# SYS command. line 497

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 500

 sambamba sort -t 1 -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.nmsrt.bam

# SYS command. line 502

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
27187 (process ID) old priority 0, new priority 19
Num 3
ID task.postalign_bam.bam_to_bedpe_rep2.line_602.id_12
Name bam_to_bedpe rep2
Thread thread_42
PID 46354
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:03:00
End 2017-04-07 17:08:17
Elapsed 00:05:16
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.nmsrt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz
Dependencies 
 
# SYS command. line 604

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 607

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.nmsrt.bam | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz

# SYS command. line 609

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
12701 (process ID) old priority 0, new priority 19
Num 4
ID task.postalign_bam.bedpe_to_tag_rep2.line_640.id_13
Name bedpe_to_tag rep2
Thread thread_42
PID 46355
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:08:18
End 2017-04-07 17:10:43
Elapsed 00:02:24
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz
Dependencies 
 
# SYS command. line 642

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 644

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz

# SYS command. line 647

 echo

# SYS command. line 649

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
14207 (process ID) old priority 0, new priority 19
Num 5
ID task.postalign_bed.subsample_bedpe2tag_rep2.line_115.id_14
Name subsample_bedpe2tag rep2
Thread thread_42
PID 46356
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:10:44
End 2017-04-07 17:12:00
Elapsed 00:01:15
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz
Dependencies 
 
# SYS command. line 117

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 121

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz

# SYS command. line 125

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
18806 (process ID) old priority 0, new priority 19
Waiting for 3 seconds.
Num 6
ID task.postalign_bed.spr_PE_rep2.line_299.id_15
Name spr_PE rep2
Thread thread_42
PID 46357
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:10:45
End 2017-04-07 17:15:27
Elapsed 00:04:41
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz
Dependencies 
 
# SYS command. line 301

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 304

 nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz | wc -l )

# SYS command. line 305

 nlines=$(( (nlines + 1) / 2 ))

# SYS command. line 309

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bedpe.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.  

# SYS command. line 312

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.00" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz

# SYS command. line 314

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.00

# SYS command. line 315

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.01" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz

# SYS command. line 317

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.01

# SYS command. line 319

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
15122 (process ID) old priority 0, new priority 19
Num 7
ID task.postalign_bed.xcor_rep2.line_212.id_16
Name xcor rep2
Thread thread_42
PID 46358
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 2
Mem
Start 2017-04-07 17:15:29
End 2017-04-07 17:25:09
Elapsed 00:09:40
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf
Dependencies 
 
# SYS command. line 214

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 217

 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 223

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc

# SYS command. line 229

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
8584 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.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: 2 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz 
opened /tmp/46358.1.q/RtmpjdrQWR/ENCFF241VRG.15M.tagAlign21c22766e7c4
done. read 15000000 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1658969 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.250439643923327,0.25042833670953 
Top 3 estimates for fragment length 240,250 
Window half size 615 
Phantom peak location 105 
Phantom peak Correlation 0.2242136 
Normalized Strand cross-correlation coefficient (NSC) 1.50961 
Relative Strand cross-correlation Coefficient (RSC) 1.449716 
Phantom Peak Quality Tag 1 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools
Num 8
ID task.postalign_bam.bam_to_bedpe_rep1.line_602.id_17
Name bam_to_bedpe rep1
Thread thread_41
PID 46359
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:27:14
End 2017-04-07 17:35:40
Elapsed 00:08:26
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.nmsrt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz
Dependencies 
 
# SYS command. line 604

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 607

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.nmsrt.bam | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz

# SYS command. line 609

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
31500 (process ID) old priority 0, new priority 19
Num 9
ID task.postalign_bam.bedpe_to_tag_rep1.line_640.id_18
Name bedpe_to_tag rep1
Thread thread_41
PID 46360
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:35:42
End 2017-04-07 17:39:32
Elapsed 00:03:50
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz
Dependencies 
 
# SYS command. line 642

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 644

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz

# SYS command. line 647

 echo

# SYS command. line 649

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
38419 (process ID) old priority 0, new priority 19
Num 10
ID task.postalign_bed.subsample_bedpe2tag_rep1.line_115.id_19
Name subsample_bedpe2tag rep1
Thread thread_41
PID 46361
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:39:33
End 2017-04-07 17:40:59
Elapsed 00:01:25
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz
Dependencies 
 
# SYS command. line 117

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 121

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz

# SYS command. line 125

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
41356 (process ID) old priority 0, new priority 19
Num 11
ID task.postalign_bed.spr_PE_rep1.line_299.id_20
Name spr_PE rep1
Thread thread_41
PID 46362
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-04-07 17:39:34
End 2017-04-07 17:45:43
Elapsed 00:06:08
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz
Dependencies 
 
# SYS command. line 301

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 304

 nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz | wc -l )

# SYS command. line 305

 nlines=$(( (nlines + 1) / 2 ))

# SYS command. line 309

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bedpe.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.  

# SYS command. line 312

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.00" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz

# SYS command. line 314

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.00

# SYS command. line 315

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.01" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz

# SYS command. line 317

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.01

# SYS command. line 319

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
41357 (process ID) old priority 0, new priority 19
Num 12
ID task.postalign_bed.xcor_rep1.line_212.id_21
Name xcor rep1
Thread thread_41
PID 46363
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 2
Mem
Start 2017-04-07 17:45:44
End 2017-04-07 17:56:01
Elapsed 00:10:16
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf
Dependencies 
 
# SYS command. line 214

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 217

 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 223

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc

# SYS command. line 229

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
56251 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.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: 2 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz 
opened /tmp/46363.1.q/RtmpFJRtXy/ENCFF066ZSK.15M.tagAligndd4e5350aa8f
done. read 15000000 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.167174 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.246658462691947 
Top 3 estimates for fragment length 235 
Window half size 630 
Phantom peak location 105 
Phantom peak Correlation 0.2228084 
Normalized Strand cross-correlation coefficient (NSC) 1.475459 
Relative Strand cross-correlation Coefficient (RSC) 1.428692 
Phantom Peak Quality Tag 1 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools
Num 13
ID task.postalign_bed.pool_tag_pooled_rep.line_436.id_22
Name pool_tag pooled_rep
Thread thread_Root
PID 46370
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-07 17:56:03
End 2017-04-07 17:56:03
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz
Dependencies 
 
# SYS command. line 438

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 440

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz

# SYS command. line 442

 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--------------------
5659 (process ID) old priority 0, new priority 19
Num 14
ID task.postalign_bed.pool_tag_ppr1.line_436.id_23
Name pool_tag ppr1
Thread thread_Root
PID 46371
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-07 17:56:04
End 2017-04-07 17:56:04
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz
Dependencies 
 
# SYS command. line 438

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 440

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz

# SYS command. line 442

 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--------------------
33182 (process ID) old priority 0, new priority 19
Num 15
ID task.postalign_bed.pool_tag_ppr2.line_436.id_24
Name pool_tag ppr2
Thread thread_Root
PID 46372
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-07 17:56:05
End 2017-04-07 17:56:05
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz
Dependencies 
 
# SYS command. line 438

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 440

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz

# SYS command. line 442

 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--------------------
22046 (process ID) old priority 0, new priority 19

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
bool allowEmpty false
string[] args [-title, ZBTB26_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, $]
bool canFail false
string CPATH /users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int cpus -1
int cpusLocal 56
int day 86400
string DEEPLIFT_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:12.0
real E 2.718281828459045
string ENHANCER_SCRIPTS_DIR /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
string EVENT_NOEPOLL 1
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KERAS_DIR /users/imk1/.local/lib/python2.7/site-packages/keras/
string KRB5CCNAME FILE:/tmp/krb5cc_1048_CCx82k
string LANG en_US.UTF-8
string LIBRARY_PATH /users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string LOADEDMODULES
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string 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/scratch/imk1/TFBindingPredictionProject/src/rcade/:/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:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts//exec:/users/imk1/edirect:/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
string PERL5LIB /users/imk1/perl5/lib/perl5
string PERL_LOCAL_LIB_ROOT /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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2
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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2
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 4
string SSH_CLIENT 171.65.77.8 57066 22
string SSH_CONNECTION 171.65.77.8 57067 171.65.76.63 22
string SSH_TTY /dev/pts/4
string STY 40931.ZBTB26_MACS2.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 TMUX /tmp/tmux-1048/default,43619,2
string TMUX_PANE %2
string USER imk1
string UTIL_SCRIPTS_DIR /srv/scratch/shared/surya/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 67062
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt