Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170413_131448_123
Start time	2017-04-13 13:14:48
Run time	02:20:22.467
Tasks executed	43
Tasks failed	0
Tasks failed names
Arguments*	[-title, EGR2_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/EGR2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170413_131448_123/task.postalign_bed.pool_tag_pooled_rep.line_436.id_16 chipseq.bds.20170413_131448_123/task.postalign_bed.pool_tag_ppr1.line_436.id_17 chipseq.bds.20170413_131448_123/task.postalign_bed.pool_tag_ppr2.line_436.id_18 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_19 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_20 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_21 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_22 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_23 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_24 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_25 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_26 chipseq.bds.20170413_131448_123/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_27 chipseq.bds.20170413_131448_123/task.callpeak_naive_overlap.naive_overlap.line_143.id_28 chipseq.bds.20170413_131448_123/task.callpeak_idr.idr2_rep1_rep2.line_74.id_29 chipseq.bds.20170413_131448_123/task.callpeak_idr.idr2_rep1_pr.line_74.id_30 chipseq.bds.20170413_131448_123/task.callpeak_idr.idr2_rep2_pr.line_74.id_31 chipseq.bds.20170413_131448_123/task.callpeak_idr.idr2_ppr.line_74.id_32 chipseq.bds.20170413_131448_123/task.sys.copy_file.line_131.id_41 chipseq.bds.20170413_131448_123/task.sys.copy_file.line_131.id_42 chipseq.bds.20170413_131448_123/task.sys.copy_file.line_131.id_43 chipseq.bds.20170413_131448_123/task.sys.copy_file.line_131.id_44 chipseq.bds.20170413_131448_123/task.callpeak_idr.idr_final_qc.line_283.id_45 chipseq.bds.20170413_131448_123/task.callpeak_idr.FRiP_rep1_pr.line_120.id_46 chipseq.bds.20170413_131448_123/task.callpeak_idr.FRiP_rep2_pr.line_120.id_47 chipseq.bds.20170413_131448_123/task.callpeak_idr.FRiP_ppr.line_120.id_48 chipseq.bds.20170413_131448_123/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_49 chipseq.bds.20170413_131448_123/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_50 chipseq.bds.20170413_131448_123/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_51 chipseq.bds.20170413_131448_123/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_52 chipseq.bds.20170413_131448_123/task.report.peak2hammock.line_361.id_55 chipseq.bds.20170413_131448_123/task.report.peak2hammock.line_361.id_56 chipseq.bds.20170413_131448_123/task.report.peak2hammock.line_361.id_57 chipseq.bds.20170413_131448_123/task.report.peak2hammock.line_361.id_58 chipseq.bds.20170413_131448_123/task.report.peak2hammock.line_361.id_59 chipseq.bds.20170413_131448_123/task.graphviz.report.line_97.id_60 chipseq.bds.20170413_131448_123/task.report.pdf2png.line_328.id_61 chipseq.bds.20170413_131448_123/task.report.pdf2png.line_328.id_62
thread_43	thread_Root
thread_42	thread_Root
thread_41	thread_Root	chipseq.bds.20170413_131448_123_parallel_41/task.postalign_bam.nmsrt_bam_rep1.line_495.id_10 chipseq.bds.20170413_131448_123_parallel_41/task.postalign_bam.bam_to_bedpe_rep1.line_602.id_11 chipseq.bds.20170413_131448_123_parallel_41/task.postalign_bam.bedpe_to_tag_rep1.line_640.id_12 chipseq.bds.20170413_131448_123_parallel_41/task.postalign_bed.subsample_bedpe2tag_rep1.line_115.id_13 chipseq.bds.20170413_131448_123_parallel_41/task.postalign_bed.spr_PE_rep1.line_299.id_14 chipseq.bds.20170413_131448_123_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_15

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	46801

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:14:52
End	2017-04-13 13:31:07
Elapsed	00:16:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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--------------------
12155 (process ID) old priority 0, new priority 19

Num	2
ID	task.postalign_bam.bam_to_bedpe_rep1.line_602.id_11
Name	bam_to_bedpe rep1
Thread	thread_41
PID	46833

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:31:08
End	2017-04-13 13:32:47
Elapsed	00:01:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.nmsrt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.nmsrt.bam | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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--------------------
12677 (process ID) old priority 0, new priority 19

Num	3
ID	task.postalign_bam.bedpe_to_tag_rep1.line_640.id_12
Name	bedpe_to_tag rep1
Thread	thread_41
PID	46835

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:32:49
End	2017-04-13 13:34:02
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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--------------------
17747 (process ID) old priority 0, new priority 19

Waiting for 20 seconds.

Num	4
ID	task.postalign_bed.subsample_bedpe2tag_rep1.line_115.id_13
Name	subsample_bedpe2tag rep1
Thread	thread_41
PID	46836

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:34:03
End	2017-04-13 13:35:16
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bedpe.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bedpe.gz | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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--------------------
18243 (process ID) old priority 0, new priority 19
Waiting for 25 seconds.

Num	5
ID	task.postalign_bed.spr_PE_rep1.line_299.id_14
Name	spr_PE rep1
Thread	thread_41
PID	46837

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:34:04
End	2017-04-13 13:35:27
Elapsed	00:01:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bedpe.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bedpe.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.  

# 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/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.00" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz

# SYS command. line 314

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.01" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz

# SYS command. line 317

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.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--------------------
12752 (process ID) old priority 0, new priority 19

Num	6
ID	task.postalign_bed.xcor_rep1.line_212.id_15
Name	xcor rep1
Thread	thread_41
PID	46840

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-04-13 13:35:28
End	2017-04-13 13:44:26
Elapsed	00:08:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.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--------------------
23458 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_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/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.15M.tagAlign.gz 
opened /tmp/46840.1.q/RtmpjrxtUb/ENCFF888DOH.15M.tagAlign5c4048d630d1
done. read 12272572 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1388623 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.237278794244713 
Top 3 estimates for fragment length 195 
Window half size 425 
Phantom peak location 105 
Phantom peak Correlation 0.209552 
Normalized Strand cross-correlation coefficient (NSC) 1.708735 
Relative Strand cross-correlation Coefficient (RSC) 1.392233 
Phantom Peak Quality Tag 1 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools

Num	7
ID	task.postalign_bed.pool_tag_pooled_rep.line_436.id_16
Name	pool_tag pooled_rep
Thread	thread_Root
PID	46850

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:44:27
End	2017-04-13 13:46:03
Elapsed	00:01:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.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

   
--------------------Stdout--------------------
21442 (process ID) old priority 0, new priority 19

Num	8
ID	task.postalign_bed.pool_tag_ppr1.line_436.id_17
Name	pool_tag ppr1
Thread	thread_Root
PID	46851

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:44:28
End	2017-04-13 13:45:45
Elapsed	00:01:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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

   
--------------------Stdout--------------------
30090 (process ID) old priority 0, new priority 19
Waiting for 28 seconds.

Num	9
ID	task.postalign_bed.pool_tag_ppr2.line_436.id_18
Name	pool_tag ppr2
Thread	thread_Root
PID	46852

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:44:30
End	2017-04-13 13:45:46
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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

   
--------------------Stdout--------------------
30089 (process ID) old priority 0, new priority 19
Waiting for 25 seconds.

Num	10
ID	task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_19
Name	macs2 n/s pooled_rep
Thread	thread_Root
PID	46853

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:46:05
End	2017-04-13 15:13:07
Elapsed	01:27:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
33623 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:46:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 13:46:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:46:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:46:19:  1000000 
INFO  @ Thu, 13 Apr 2017 13:46:20:  2000000 
INFO  @ Thu, 13 Apr 2017 13:46:22:  3000000 
INFO  @ Thu, 13 Apr 2017 13:46:24:  4000000 
INFO  @ Thu, 13 Apr 2017 13:46:25:  5000000 
INFO  @ Thu, 13 Apr 2017 13:46:27:  6000000 
INFO  @ Thu, 13 Apr 2017 13:46:28:  7000000 
INFO  @ Thu, 13 Apr 2017 13:46:30:  8000000 
INFO  @ Thu, 13 Apr 2017 13:46:32:  9000000 
INFO  @ Thu, 13 Apr 2017 13:46:33:  10000000 
INFO  @ Thu, 13 Apr 2017 13:46:35:  11000000 
INFO  @ Thu, 13 Apr 2017 13:46:36:  12000000 
INFO  @ Thu, 13 Apr 2017 13:46:38:  13000000 
INFO  @ Thu, 13 Apr 2017 13:46:39:  14000000 
INFO  @ Thu, 13 Apr 2017 13:46:41:  15000000 
INFO  @ Thu, 13 Apr 2017 13:46:43:  16000000 
INFO  @ Thu, 13 Apr 2017 13:46:44:  17000000 
INFO  @ Thu, 13 Apr 2017 13:46:46:  18000000 
INFO  @ Thu, 13 Apr 2017 13:46:47:  19000000 
INFO  @ Thu, 13 Apr 2017 13:46:49:  20000000 
INFO  @ Thu, 13 Apr 2017 13:46:50:  21000000 
INFO  @ Thu, 13 Apr 2017 13:46:52:  22000000 
INFO  @ Thu, 13 Apr 2017 13:46:53:  23000000 
INFO  @ Thu, 13 Apr 2017 13:46:55:  24000000 
INFO  @ Thu, 13 Apr 2017 13:46:57:  25000000 
INFO  @ Thu, 13 Apr 2017 13:46:58:  26000000 
INFO  @ Thu, 13 Apr 2017 13:47:00:  27000000 
INFO  @ Thu, 13 Apr 2017 13:47:01:  28000000 
INFO  @ Thu, 13 Apr 2017 13:47:03:  29000000 
INFO  @ Thu, 13 Apr 2017 13:47:04:  30000000 
INFO  @ Thu, 13 Apr 2017 13:47:06:  31000000 
INFO  @ Thu, 13 Apr 2017 13:47:08:  32000000 
INFO  @ Thu, 13 Apr 2017 13:47:09:  33000000 
INFO  @ Thu, 13 Apr 2017 13:47:11:  34000000 
INFO  @ Thu, 13 Apr 2017 13:47:12:  35000000 
INFO  @ Thu, 13 Apr 2017 13:47:14:  36000000 
INFO  @ Thu, 13 Apr 2017 13:47:15:  37000000 
INFO  @ Thu, 13 Apr 2017 13:47:17:  38000000 
INFO  @ Thu, 13 Apr 2017 13:47:19:  39000000 
INFO  @ Thu, 13 Apr 2017 13:47:20:  40000000 
INFO  @ Thu, 13 Apr 2017 13:47:22:  41000000 
INFO  @ Thu, 13 Apr 2017 13:47:23:  42000000 
INFO  @ Thu, 13 Apr 2017 13:47:25:  43000000 
INFO  @ Thu, 13 Apr 2017 13:47:26:  44000000 
INFO  @ Thu, 13 Apr 2017 13:47:28:  45000000 
INFO  @ Thu, 13 Apr 2017 13:47:31: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:47:33:  1000000 
INFO  @ Thu, 13 Apr 2017 13:47:34:  2000000 
INFO  @ Thu, 13 Apr 2017 13:47:36:  3000000 
INFO  @ Thu, 13 Apr 2017 13:47:37:  4000000 
INFO  @ Thu, 13 Apr 2017 13:47:39:  5000000 
INFO  @ Thu, 13 Apr 2017 13:47:40:  6000000 
INFO  @ Thu, 13 Apr 2017 13:47:41:  7000000 
INFO  @ Thu, 13 Apr 2017 13:47:43:  8000000 
INFO  @ Thu, 13 Apr 2017 13:47:44:  9000000 
INFO  @ Thu, 13 Apr 2017 13:47:46:  10000000 
INFO  @ Thu, 13 Apr 2017 13:47:47:  11000000 
INFO  @ Thu, 13 Apr 2017 13:47:48:  12000000 
INFO  @ Thu, 13 Apr 2017 13:47:50:  13000000 
INFO  @ Thu, 13 Apr 2017 13:47:51:  14000000 
INFO  @ Thu, 13 Apr 2017 13:47:53:  15000000 
INFO  @ Thu, 13 Apr 2017 13:47:54:  16000000 
INFO  @ Thu, 13 Apr 2017 13:47:55:  17000000 
INFO  @ Thu, 13 Apr 2017 13:47:57:  18000000 
INFO  @ Thu, 13 Apr 2017 13:47:58:  19000000 
INFO  @ Thu, 13 Apr 2017 13:48:00:  20000000 
INFO  @ Thu, 13 Apr 2017 13:48:01:  21000000 
INFO  @ Thu, 13 Apr 2017 13:48:03:  22000000 
INFO  @ Thu, 13 Apr 2017 13:48:04:  23000000 
INFO  @ Thu, 13 Apr 2017 13:48:05:  24000000 
INFO  @ Thu, 13 Apr 2017 13:48:07:  25000000 
INFO  @ Thu, 13 Apr 2017 13:48:08:  26000000 
INFO  @ Thu, 13 Apr 2017 13:48:10:  27000000 
INFO  @ Thu, 13 Apr 2017 13:48:11:  28000000 
INFO  @ Thu, 13 Apr 2017 13:48:12:  29000000 
INFO  @ Thu, 13 Apr 2017 13:48:14:  30000000 
INFO  @ Thu, 13 Apr 2017 13:48:15:  31000000 
INFO  @ Thu, 13 Apr 2017 13:48:17:  32000000 
INFO  @ Thu, 13 Apr 2017 13:48:18:  33000000 
INFO  @ Thu, 13 Apr 2017 13:48:19:  34000000 
INFO  @ Thu, 13 Apr 2017 13:48:21:  35000000 
INFO  @ Thu, 13 Apr 2017 13:48:22:  36000000 
INFO  @ Thu, 13 Apr 2017 13:48:24:  37000000 
INFO  @ Thu, 13 Apr 2017 13:48:25:  38000000 
INFO  @ Thu, 13 Apr 2017 13:48:27:  39000000 
INFO  @ Thu, 13 Apr 2017 13:48:28:  40000000 
INFO  @ Thu, 13 Apr 2017 13:48:29:  41000000 
INFO  @ Thu, 13 Apr 2017 13:48:31:  42000000 
INFO  @ Thu, 13 Apr 2017 13:48:32:  43000000 
INFO  @ Thu, 13 Apr 2017 13:48:34:  44000000 
INFO  @ Thu, 13 Apr 2017 13:48:35:  45000000 
INFO  @ Thu, 13 Apr 2017 13:48:36:  46000000 
INFO  @ Thu, 13 Apr 2017 13:48:38:  47000000 
INFO  @ Thu, 13 Apr 2017 13:48:39:  48000000 
INFO  @ Thu, 13 Apr 2017 13:48:41:  49000000 
INFO  @ Thu, 13 Apr 2017 13:48:42:  50000000 
INFO  @ Thu, 13 Apr 2017 13:48:43:  51000000 
INFO  @ Thu, 13 Apr 2017 13:48:45:  52000000 
INFO  @ Thu, 13 Apr 2017 13:48:46:  53000000 
INFO  @ Thu, 13 Apr 2017 13:48:47:  54000000 
INFO  @ Thu, 13 Apr 2017 13:48:49:  55000000 
INFO  @ Thu, 13 Apr 2017 13:48:50:  56000000 
INFO  @ Thu, 13 Apr 2017 13:48:52:  57000000 
INFO  @ Thu, 13 Apr 2017 13:48:53:  58000000 
INFO  @ Thu, 13 Apr 2017 13:48:55:  59000000 
INFO  @ Thu, 13 Apr 2017 13:48:56:  60000000 
INFO  @ Thu, 13 Apr 2017 13:48:57:  61000000 
INFO  @ Thu, 13 Apr 2017 13:48:59:  62000000 
INFO  @ Thu, 13 Apr 2017 13:49:00:  63000000 
INFO  @ Thu, 13 Apr 2017 13:49:02:  64000000 
INFO  @ Thu, 13 Apr 2017 13:49:03:  65000000 
INFO  @ Thu, 13 Apr 2017 13:49:04:  66000000 
INFO  @ Thu, 13 Apr 2017 13:49:06:  67000000 
INFO  @ Thu, 13 Apr 2017 13:49:08:  68000000 
INFO  @ Thu, 13 Apr 2017 13:49:09:  69000000 
INFO  @ Thu, 13 Apr 2017 13:49:10:  70000000 
INFO  @ Thu, 13 Apr 2017 13:49:12:  71000000 
INFO  @ Thu, 13 Apr 2017 13:49:13:  72000000 
INFO  @ Thu, 13 Apr 2017 13:49:15:  73000000 
INFO  @ Thu, 13 Apr 2017 13:49:16:  74000000 
INFO  @ Thu, 13 Apr 2017 13:49:18:  75000000 
INFO  @ Thu, 13 Apr 2017 13:49:19:  76000000 
INFO  @ Thu, 13 Apr 2017 13:49:21:  77000000 
INFO  @ Thu, 13 Apr 2017 13:49:22:  78000000 
INFO  @ Thu, 13 Apr 2017 13:49:24:  79000000 
INFO  @ Thu, 13 Apr 2017 13:49:25:  80000000 
INFO  @ Thu, 13 Apr 2017 13:49:26:  81000000 
INFO  @ Thu, 13 Apr 2017 13:49:28:  82000000 
INFO  @ Thu, 13 Apr 2017 13:49:29:  83000000 
INFO  @ Thu, 13 Apr 2017 13:49:31:  84000000 
INFO  @ Thu, 13 Apr 2017 13:49:32:  85000000 
INFO  @ Thu, 13 Apr 2017 13:49:34:  86000000 
INFO  @ Thu, 13 Apr 2017 13:49:35:  87000000 
INFO  @ Thu, 13 Apr 2017 13:49:37:  88000000 
INFO  @ Thu, 13 Apr 2017 13:49:38:  89000000 
INFO  @ Thu, 13 Apr 2017 13:49:39:  90000000 
INFO  @ Thu, 13 Apr 2017 13:49:41:  91000000 
INFO  @ Thu, 13 Apr 2017 13:49:42:  92000000 
INFO  @ Thu, 13 Apr 2017 13:49:44:  93000000 
INFO  @ Thu, 13 Apr 2017 13:49:45:  94000000 
INFO  @ Thu, 13 Apr 2017 13:49:47:  95000000 
INFO  @ Thu, 13 Apr 2017 13:49:48:  96000000 
INFO  @ Thu, 13 Apr 2017 13:49:49:  97000000 
INFO  @ Thu, 13 Apr 2017 13:49:51:  98000000 
INFO  @ Thu, 13 Apr 2017 13:49:52:  99000000 
INFO  @ Thu, 13 Apr 2017 13:49:54: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:49:54: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:49:54: #1  total tags in treatment: 45202518 
INFO  @ Thu, 13 Apr 2017 13:49:54: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:49:54: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:49:54: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:49:54: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:49:54: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:49:54: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:49:54: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:49:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:55:41: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:55:41: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:55:41: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:55:41: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:55:41: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:04:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:04:42: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:04:42: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:04:43: Done! 
INFO  @ Thu, 13 Apr 2017 14:04:46: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:06:09: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:08:50: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:09:55: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:19:01: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:25:25: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:39:35: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:40:56: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:43:31: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:44:34: Values in your input bedGraph files will be multiplied by 45.202518 ... 
INFO  @ Thu, 13 Apr 2017 14:53:52: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 14:55:38: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:00:49: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'!

Num	11
ID	task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_20
Name	macs2 n/s ppr1
Thread	thread_Root
PID	46854

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:46:06
End	2017-04-13 14:09:09
Elapsed	00:23:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
22379 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:46:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 13:46:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:46:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:46:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:46:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:46:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:46:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:46:43:  5000000 
INFO  @ Thu, 13 Apr 2017 13:46:45:  6000000 
INFO  @ Thu, 13 Apr 2017 13:46:47:  7000000 
INFO  @ Thu, 13 Apr 2017 13:46:49:  8000000 
INFO  @ Thu, 13 Apr 2017 13:46:51:  9000000 
INFO  @ Thu, 13 Apr 2017 13:46:53:  10000000 
INFO  @ Thu, 13 Apr 2017 13:46:55:  11000000 
INFO  @ Thu, 13 Apr 2017 13:46:58:  12000000 
INFO  @ Thu, 13 Apr 2017 13:47:00:  13000000 
INFO  @ Thu, 13 Apr 2017 13:47:02:  14000000 
INFO  @ Thu, 13 Apr 2017 13:47:04:  15000000 
INFO  @ Thu, 13 Apr 2017 13:47:06:  16000000 
INFO  @ Thu, 13 Apr 2017 13:47:08:  17000000 
INFO  @ Thu, 13 Apr 2017 13:47:10:  18000000 
INFO  @ Thu, 13 Apr 2017 13:47:12:  19000000 
INFO  @ Thu, 13 Apr 2017 13:47:14:  20000000 
INFO  @ Thu, 13 Apr 2017 13:47:16:  21000000 
INFO  @ Thu, 13 Apr 2017 13:47:18:  22000000 
INFO  @ Thu, 13 Apr 2017 13:47:22: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:47:23:  1000000 
INFO  @ Thu, 13 Apr 2017 13:47:25:  2000000 
INFO  @ Thu, 13 Apr 2017 13:47:27:  3000000 
INFO  @ Thu, 13 Apr 2017 13:47:29:  4000000 
INFO  @ Thu, 13 Apr 2017 13:47:31:  5000000 
INFO  @ Thu, 13 Apr 2017 13:47:33:  6000000 
INFO  @ Thu, 13 Apr 2017 13:47:35:  7000000 
INFO  @ Thu, 13 Apr 2017 13:47:37:  8000000 
INFO  @ Thu, 13 Apr 2017 13:47:39:  9000000 
INFO  @ Thu, 13 Apr 2017 13:47:41:  10000000 
INFO  @ Thu, 13 Apr 2017 13:47:43:  11000000 
INFO  @ Thu, 13 Apr 2017 13:47:44:  12000000 
INFO  @ Thu, 13 Apr 2017 13:47:46:  13000000 
INFO  @ Thu, 13 Apr 2017 13:47:48:  14000000 
INFO  @ Thu, 13 Apr 2017 13:47:50:  15000000 
INFO  @ Thu, 13 Apr 2017 13:47:52:  16000000 
INFO  @ Thu, 13 Apr 2017 13:47:54:  17000000 
INFO  @ Thu, 13 Apr 2017 13:47:56:  18000000 
INFO  @ Thu, 13 Apr 2017 13:47:58:  19000000 
INFO  @ Thu, 13 Apr 2017 13:48:00:  20000000 
INFO  @ Thu, 13 Apr 2017 13:48:02:  21000000 
INFO  @ Thu, 13 Apr 2017 13:48:04:  22000000 
INFO  @ Thu, 13 Apr 2017 13:48:06:  23000000 
INFO  @ Thu, 13 Apr 2017 13:48:08:  24000000 
INFO  @ Thu, 13 Apr 2017 13:48:10:  25000000 
INFO  @ Thu, 13 Apr 2017 13:48:12:  26000000 
INFO  @ Thu, 13 Apr 2017 13:48:14:  27000000 
INFO  @ Thu, 13 Apr 2017 13:48:16:  28000000 
INFO  @ Thu, 13 Apr 2017 13:48:18:  29000000 
INFO  @ Thu, 13 Apr 2017 13:48:20:  30000000 
INFO  @ Thu, 13 Apr 2017 13:48:22:  31000000 
INFO  @ Thu, 13 Apr 2017 13:48:24:  32000000 
INFO  @ Thu, 13 Apr 2017 13:48:26:  33000000 
INFO  @ Thu, 13 Apr 2017 13:48:28:  34000000 
INFO  @ Thu, 13 Apr 2017 13:48:30:  35000000 
INFO  @ Thu, 13 Apr 2017 13:48:32:  36000000 
INFO  @ Thu, 13 Apr 2017 13:48:34:  37000000 
INFO  @ Thu, 13 Apr 2017 13:48:36:  38000000 
INFO  @ Thu, 13 Apr 2017 13:48:38:  39000000 
INFO  @ Thu, 13 Apr 2017 13:48:40:  40000000 
INFO  @ Thu, 13 Apr 2017 13:48:42:  41000000 
INFO  @ Thu, 13 Apr 2017 13:48:44:  42000000 
INFO  @ Thu, 13 Apr 2017 13:48:46:  43000000 
INFO  @ Thu, 13 Apr 2017 13:48:48:  44000000 
INFO  @ Thu, 13 Apr 2017 13:48:50:  45000000 
INFO  @ Thu, 13 Apr 2017 13:48:52:  46000000 
INFO  @ Thu, 13 Apr 2017 13:48:54:  47000000 
INFO  @ Thu, 13 Apr 2017 13:48:56:  48000000 
INFO  @ Thu, 13 Apr 2017 13:48:58:  49000000 
INFO  @ Thu, 13 Apr 2017 13:49:00:  50000000 
INFO  @ Thu, 13 Apr 2017 13:49:02:  51000000 
INFO  @ Thu, 13 Apr 2017 13:49:04:  52000000 
INFO  @ Thu, 13 Apr 2017 13:49:06:  53000000 
INFO  @ Thu, 13 Apr 2017 13:49:08:  54000000 
INFO  @ Thu, 13 Apr 2017 13:49:10:  55000000 
INFO  @ Thu, 13 Apr 2017 13:49:12:  56000000 
INFO  @ Thu, 13 Apr 2017 13:49:14:  57000000 
INFO  @ Thu, 13 Apr 2017 13:49:16:  58000000 
INFO  @ Thu, 13 Apr 2017 13:49:18:  59000000 
INFO  @ Thu, 13 Apr 2017 13:49:20:  60000000 
INFO  @ Thu, 13 Apr 2017 13:49:22:  61000000 
INFO  @ Thu, 13 Apr 2017 13:49:24:  62000000 
INFO  @ Thu, 13 Apr 2017 13:49:26:  63000000 
INFO  @ Thu, 13 Apr 2017 13:49:28:  64000000 
INFO  @ Thu, 13 Apr 2017 13:49:30:  65000000 
INFO  @ Thu, 13 Apr 2017 13:49:32:  66000000 
INFO  @ Thu, 13 Apr 2017 13:49:34:  67000000 
INFO  @ Thu, 13 Apr 2017 13:49:36:  68000000 
INFO  @ Thu, 13 Apr 2017 13:49:37:  69000000 
INFO  @ Thu, 13 Apr 2017 13:49:39:  70000000 
INFO  @ Thu, 13 Apr 2017 13:49:41:  71000000 
INFO  @ Thu, 13 Apr 2017 13:49:43:  72000000 
INFO  @ Thu, 13 Apr 2017 13:49:45:  73000000 
INFO  @ Thu, 13 Apr 2017 13:49:47:  74000000 
INFO  @ Thu, 13 Apr 2017 13:49:49:  75000000 
INFO  @ Thu, 13 Apr 2017 13:49:51:  76000000 
INFO  @ Thu, 13 Apr 2017 13:49:53:  77000000 
INFO  @ Thu, 13 Apr 2017 13:49:55:  78000000 
INFO  @ Thu, 13 Apr 2017 13:49:57:  79000000 
INFO  @ Thu, 13 Apr 2017 13:49:59:  80000000 
INFO  @ Thu, 13 Apr 2017 13:50:01:  81000000 
INFO  @ Thu, 13 Apr 2017 13:50:03:  82000000 
INFO  @ Thu, 13 Apr 2017 13:50:05:  83000000 
INFO  @ Thu, 13 Apr 2017 13:50:07:  84000000 
INFO  @ Thu, 13 Apr 2017 13:50:09:  85000000 
INFO  @ Thu, 13 Apr 2017 13:50:11:  86000000 
INFO  @ Thu, 13 Apr 2017 13:50:13:  87000000 
INFO  @ Thu, 13 Apr 2017 13:50:15:  88000000 
INFO  @ Thu, 13 Apr 2017 13:50:17:  89000000 
INFO  @ Thu, 13 Apr 2017 13:50:19:  90000000 
INFO  @ Thu, 13 Apr 2017 13:50:21:  91000000 
INFO  @ Thu, 13 Apr 2017 13:50:23:  92000000 
INFO  @ Thu, 13 Apr 2017 13:50:25:  93000000 
INFO  @ Thu, 13 Apr 2017 13:50:27:  94000000 
INFO  @ Thu, 13 Apr 2017 13:50:29:  95000000 
INFO  @ Thu, 13 Apr 2017 13:50:31:  96000000 
INFO  @ Thu, 13 Apr 2017 13:50:33:  97000000 
INFO  @ Thu, 13 Apr 2017 13:50:35:  98000000 
INFO  @ Thu, 13 Apr 2017 13:50:37:  99000000 
INFO  @ Thu, 13 Apr 2017 13:50:39: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:50:39: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:50:39: #1  total tags in treatment: 22601260 
INFO  @ Thu, 13 Apr 2017 13:50:39: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:50:39: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:50:39: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:50:39: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:50:39: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:50:39: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:50:39: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:50:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:57:29: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:57:29: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:57:29: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:57:29: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:57:29: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:08:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:09:00: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:09:03: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:09:05: Done!

Num	12
ID	task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_21
Name	macs2 n/s ppr2
Thread	thread_Root
PID	46855

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:46:08
End	2017-04-13 14:02:38
Elapsed	00:16:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
34369 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:46:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 13:46:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:46:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:46:34:  1000000 
INFO  @ Thu, 13 Apr 2017 13:46:35:  2000000 
INFO  @ Thu, 13 Apr 2017 13:46:37:  3000000 
INFO  @ Thu, 13 Apr 2017 13:46:38:  4000000 
INFO  @ Thu, 13 Apr 2017 13:46:40:  5000000 
INFO  @ Thu, 13 Apr 2017 13:46:41:  6000000 
INFO  @ Thu, 13 Apr 2017 13:46:43:  7000000 
INFO  @ Thu, 13 Apr 2017 13:46:44:  8000000 
INFO  @ Thu, 13 Apr 2017 13:46:46:  9000000 
INFO  @ Thu, 13 Apr 2017 13:46:47:  10000000 
INFO  @ Thu, 13 Apr 2017 13:46:49:  11000000 
INFO  @ Thu, 13 Apr 2017 13:46:50:  12000000 
INFO  @ Thu, 13 Apr 2017 13:46:52:  13000000 
INFO  @ Thu, 13 Apr 2017 13:46:53:  14000000 
INFO  @ Thu, 13 Apr 2017 13:46:55:  15000000 
INFO  @ Thu, 13 Apr 2017 13:46:56:  16000000 
INFO  @ Thu, 13 Apr 2017 13:46:58:  17000000 
INFO  @ Thu, 13 Apr 2017 13:46:59:  18000000 
INFO  @ Thu, 13 Apr 2017 13:47:01:  19000000 
INFO  @ Thu, 13 Apr 2017 13:47:02:  20000000 
INFO  @ Thu, 13 Apr 2017 13:47:04:  21000000 
INFO  @ Thu, 13 Apr 2017 13:47:05:  22000000 
INFO  @ Thu, 13 Apr 2017 13:47:08: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:47:09:  1000000 
INFO  @ Thu, 13 Apr 2017 13:47:10:  2000000 
INFO  @ Thu, 13 Apr 2017 13:47:12:  3000000 
INFO  @ Thu, 13 Apr 2017 13:47:13:  4000000 
INFO  @ Thu, 13 Apr 2017 13:47:15:  5000000 
INFO  @ Thu, 13 Apr 2017 13:47:16:  6000000 
INFO  @ Thu, 13 Apr 2017 13:47:17:  7000000 
INFO  @ Thu, 13 Apr 2017 13:47:19:  8000000 
INFO  @ Thu, 13 Apr 2017 13:47:20:  9000000 
INFO  @ Thu, 13 Apr 2017 13:47:22:  10000000 
INFO  @ Thu, 13 Apr 2017 13:47:23:  11000000 
INFO  @ Thu, 13 Apr 2017 13:47:24:  12000000 
INFO  @ Thu, 13 Apr 2017 13:47:26:  13000000 
INFO  @ Thu, 13 Apr 2017 13:47:27:  14000000 
INFO  @ Thu, 13 Apr 2017 13:47:29:  15000000 
INFO  @ Thu, 13 Apr 2017 13:47:30:  16000000 
INFO  @ Thu, 13 Apr 2017 13:47:32:  17000000 
INFO  @ Thu, 13 Apr 2017 13:47:33:  18000000 
INFO  @ Thu, 13 Apr 2017 13:47:34:  19000000 
INFO  @ Thu, 13 Apr 2017 13:47:36:  20000000 
INFO  @ Thu, 13 Apr 2017 13:47:37:  21000000 
INFO  @ Thu, 13 Apr 2017 13:47:39:  22000000 
INFO  @ Thu, 13 Apr 2017 13:47:40:  23000000 
INFO  @ Thu, 13 Apr 2017 13:47:42:  24000000 
INFO  @ Thu, 13 Apr 2017 13:47:43:  25000000 
INFO  @ Thu, 13 Apr 2017 13:47:44:  26000000 
INFO  @ Thu, 13 Apr 2017 13:47:46:  27000000 
INFO  @ Thu, 13 Apr 2017 13:47:47:  28000000 
INFO  @ Thu, 13 Apr 2017 13:47:49:  29000000 
INFO  @ Thu, 13 Apr 2017 13:47:50:  30000000 
INFO  @ Thu, 13 Apr 2017 13:47:51:  31000000 
INFO  @ Thu, 13 Apr 2017 13:47:53:  32000000 
INFO  @ Thu, 13 Apr 2017 13:47:54:  33000000 
INFO  @ Thu, 13 Apr 2017 13:47:56:  34000000 
INFO  @ Thu, 13 Apr 2017 13:47:57:  35000000 
INFO  @ Thu, 13 Apr 2017 13:47:58:  36000000 
INFO  @ Thu, 13 Apr 2017 13:48:00:  37000000 
INFO  @ Thu, 13 Apr 2017 13:48:01:  38000000 
INFO  @ Thu, 13 Apr 2017 13:48:03:  39000000 
INFO  @ Thu, 13 Apr 2017 13:48:04:  40000000 
INFO  @ Thu, 13 Apr 2017 13:48:06:  41000000 
INFO  @ Thu, 13 Apr 2017 13:48:07:  42000000 
INFO  @ Thu, 13 Apr 2017 13:48:08:  43000000 
INFO  @ Thu, 13 Apr 2017 13:48:10:  44000000 
INFO  @ Thu, 13 Apr 2017 13:48:11:  45000000 
INFO  @ Thu, 13 Apr 2017 13:48:13:  46000000 
INFO  @ Thu, 13 Apr 2017 13:48:14:  47000000 
INFO  @ Thu, 13 Apr 2017 13:48:15:  48000000 
INFO  @ Thu, 13 Apr 2017 13:48:17:  49000000 
INFO  @ Thu, 13 Apr 2017 13:48:18:  50000000 
INFO  @ Thu, 13 Apr 2017 13:48:20:  51000000 
INFO  @ Thu, 13 Apr 2017 13:48:21:  52000000 
INFO  @ Thu, 13 Apr 2017 13:48:23:  53000000 
INFO  @ Thu, 13 Apr 2017 13:48:24:  54000000 
INFO  @ Thu, 13 Apr 2017 13:48:25:  55000000 
INFO  @ Thu, 13 Apr 2017 13:48:27:  56000000 
INFO  @ Thu, 13 Apr 2017 13:48:28:  57000000 
INFO  @ Thu, 13 Apr 2017 13:48:30:  58000000 
INFO  @ Thu, 13 Apr 2017 13:48:31:  59000000 
INFO  @ Thu, 13 Apr 2017 13:48:33:  60000000 
INFO  @ Thu, 13 Apr 2017 13:48:34:  61000000 
INFO  @ Thu, 13 Apr 2017 13:48:35:  62000000 
INFO  @ Thu, 13 Apr 2017 13:48:37:  63000000 
INFO  @ Thu, 13 Apr 2017 13:48:38:  64000000 
INFO  @ Thu, 13 Apr 2017 13:48:40:  65000000 
INFO  @ Thu, 13 Apr 2017 13:48:41:  66000000 
INFO  @ Thu, 13 Apr 2017 13:48:42:  67000000 
INFO  @ Thu, 13 Apr 2017 13:48:44:  68000000 
INFO  @ Thu, 13 Apr 2017 13:48:45:  69000000 
INFO  @ Thu, 13 Apr 2017 13:48:47:  70000000 
INFO  @ Thu, 13 Apr 2017 13:48:48:  71000000 
INFO  @ Thu, 13 Apr 2017 13:48:50:  72000000 
INFO  @ Thu, 13 Apr 2017 13:48:51:  73000000 
INFO  @ Thu, 13 Apr 2017 13:48:52:  74000000 
INFO  @ Thu, 13 Apr 2017 13:48:54:  75000000 
INFO  @ Thu, 13 Apr 2017 13:48:55:  76000000 
INFO  @ Thu, 13 Apr 2017 13:48:57:  77000000 
INFO  @ Thu, 13 Apr 2017 13:48:58:  78000000 
INFO  @ Thu, 13 Apr 2017 13:49:00:  79000000 
INFO  @ Thu, 13 Apr 2017 13:49:01:  80000000 
INFO  @ Thu, 13 Apr 2017 13:49:02:  81000000 
INFO  @ Thu, 13 Apr 2017 13:49:04:  82000000 
INFO  @ Thu, 13 Apr 2017 13:49:05:  83000000 
INFO  @ Thu, 13 Apr 2017 13:49:07:  84000000 
INFO  @ Thu, 13 Apr 2017 13:49:08:  85000000 
INFO  @ Thu, 13 Apr 2017 13:49:10:  86000000 
INFO  @ Thu, 13 Apr 2017 13:49:11:  87000000 
INFO  @ Thu, 13 Apr 2017 13:49:12:  88000000 
INFO  @ Thu, 13 Apr 2017 13:49:14:  89000000 
INFO  @ Thu, 13 Apr 2017 13:49:15:  90000000 
INFO  @ Thu, 13 Apr 2017 13:49:17:  91000000 
INFO  @ Thu, 13 Apr 2017 13:49:18:  92000000 
INFO  @ Thu, 13 Apr 2017 13:49:20:  93000000 
INFO  @ Thu, 13 Apr 2017 13:49:21:  94000000 
INFO  @ Thu, 13 Apr 2017 13:49:22:  95000000 
INFO  @ Thu, 13 Apr 2017 13:49:24:  96000000 
INFO  @ Thu, 13 Apr 2017 13:49:25:  97000000 
INFO  @ Thu, 13 Apr 2017 13:49:27:  98000000 
INFO  @ Thu, 13 Apr 2017 13:49:28:  99000000 
INFO  @ Thu, 13 Apr 2017 13:49:29: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:49:29: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:49:29: #1  total tags in treatment: 22601258 
INFO  @ Thu, 13 Apr 2017 13:49:29: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:49:29: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:49:29: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:49:29: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:49:29: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:49:29: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:49:29: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:49:29: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:54:34: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:54:34: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:54:34: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:54:34: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:54:34: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:02:33: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:02:34: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:02:35: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:02:35: Done!

Num	13
ID	task.callpeak_macs2.macs2_n_s_rep1.line_66.id_22
Name	macs2 n/s rep1
Thread	thread_Root
PID	46856

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:46:09
End	2017-04-13 15:20:43
Elapsed	01:34:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 195 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1 -o "ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1 -o "ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
22380 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:46:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 195 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 13:46:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:46:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:46:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:46:37:  2000000 
INFO  @ Thu, 13 Apr 2017 13:46:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:46:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:46:43:  5000000 
INFO  @ Thu, 13 Apr 2017 13:46:45:  6000000 
INFO  @ Thu, 13 Apr 2017 13:46:47:  7000000 
INFO  @ Thu, 13 Apr 2017 13:46:50:  8000000 
INFO  @ Thu, 13 Apr 2017 13:46:52:  9000000 
INFO  @ Thu, 13 Apr 2017 13:46:54:  10000000 
INFO  @ Thu, 13 Apr 2017 13:46:56:  11000000 
INFO  @ Thu, 13 Apr 2017 13:46:58:  12000000 
INFO  @ Thu, 13 Apr 2017 13:47:00:  13000000 
INFO  @ Thu, 13 Apr 2017 13:47:02:  14000000 
INFO  @ Thu, 13 Apr 2017 13:47:04:  15000000 
INFO  @ Thu, 13 Apr 2017 13:47:06:  16000000 
INFO  @ Thu, 13 Apr 2017 13:47:09:  17000000 
INFO  @ Thu, 13 Apr 2017 13:47:11:  18000000 
INFO  @ Thu, 13 Apr 2017 13:47:13:  19000000 
INFO  @ Thu, 13 Apr 2017 13:47:15:  20000000 
INFO  @ Thu, 13 Apr 2017 13:47:17:  21000000 
INFO  @ Thu, 13 Apr 2017 13:47:19:  22000000 
INFO  @ Thu, 13 Apr 2017 13:47:21:  23000000 
INFO  @ Thu, 13 Apr 2017 13:47:24:  24000000 
INFO  @ Thu, 13 Apr 2017 13:47:27: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:47:29:  1000000 
INFO  @ Thu, 13 Apr 2017 13:47:31:  2000000 
INFO  @ Thu, 13 Apr 2017 13:47:33:  3000000 
INFO  @ Thu, 13 Apr 2017 13:47:34:  4000000 
INFO  @ Thu, 13 Apr 2017 13:47:36:  5000000 
INFO  @ Thu, 13 Apr 2017 13:47:38:  6000000 
INFO  @ Thu, 13 Apr 2017 13:47:40:  7000000 
INFO  @ Thu, 13 Apr 2017 13:47:42:  8000000 
INFO  @ Thu, 13 Apr 2017 13:47:44:  9000000 
INFO  @ Thu, 13 Apr 2017 13:47:46:  10000000 
INFO  @ Thu, 13 Apr 2017 13:47:48:  11000000 
INFO  @ Thu, 13 Apr 2017 13:47:50:  12000000 
INFO  @ Thu, 13 Apr 2017 13:47:52:  13000000 
INFO  @ Thu, 13 Apr 2017 13:47:54:  14000000 
INFO  @ Thu, 13 Apr 2017 13:47:56:  15000000 
INFO  @ Thu, 13 Apr 2017 13:47:58:  16000000 
INFO  @ Thu, 13 Apr 2017 13:48:00:  17000000 
INFO  @ Thu, 13 Apr 2017 13:48:02:  18000000 
INFO  @ Thu, 13 Apr 2017 13:48:04:  19000000 
INFO  @ Thu, 13 Apr 2017 13:48:06:  20000000 
INFO  @ Thu, 13 Apr 2017 13:48:08:  21000000 
INFO  @ Thu, 13 Apr 2017 13:48:09:  22000000 
INFO  @ Thu, 13 Apr 2017 13:48:11:  23000000 
INFO  @ Thu, 13 Apr 2017 13:48:13:  24000000 
INFO  @ Thu, 13 Apr 2017 13:48:15:  25000000 
INFO  @ Thu, 13 Apr 2017 13:48:17:  26000000 
INFO  @ Thu, 13 Apr 2017 13:48:18:  27000000 
INFO  @ Thu, 13 Apr 2017 13:48:20:  28000000 
INFO  @ Thu, 13 Apr 2017 13:48:22:  29000000 
INFO  @ Thu, 13 Apr 2017 13:48:24:  30000000 
INFO  @ Thu, 13 Apr 2017 13:48:26:  31000000 
INFO  @ Thu, 13 Apr 2017 13:48:27:  32000000 
INFO  @ Thu, 13 Apr 2017 13:48:29:  33000000 
INFO  @ Thu, 13 Apr 2017 13:48:31:  34000000 
INFO  @ Thu, 13 Apr 2017 13:48:33:  35000000 
INFO  @ Thu, 13 Apr 2017 13:48:35:  36000000 
INFO  @ Thu, 13 Apr 2017 13:48:37:  37000000 
INFO  @ Thu, 13 Apr 2017 13:48:38:  38000000 
INFO  @ Thu, 13 Apr 2017 13:48:40:  39000000 
INFO  @ Thu, 13 Apr 2017 13:48:42:  40000000 
INFO  @ Thu, 13 Apr 2017 13:48:44:  41000000 
INFO  @ Thu, 13 Apr 2017 13:48:46:  42000000 
INFO  @ Thu, 13 Apr 2017 13:48:47:  43000000 
INFO  @ Thu, 13 Apr 2017 13:48:49:  44000000 
INFO  @ Thu, 13 Apr 2017 13:48:51:  45000000 
INFO  @ Thu, 13 Apr 2017 13:48:53:  46000000 
INFO  @ Thu, 13 Apr 2017 13:48:55:  47000000 
INFO  @ Thu, 13 Apr 2017 13:48:56:  48000000 
INFO  @ Thu, 13 Apr 2017 13:48:58:  49000000 
INFO  @ Thu, 13 Apr 2017 13:49:00:  50000000 
INFO  @ Thu, 13 Apr 2017 13:49:02:  51000000 
INFO  @ Thu, 13 Apr 2017 13:49:04:  52000000 
INFO  @ Thu, 13 Apr 2017 13:49:05:  53000000 
INFO  @ Thu, 13 Apr 2017 13:49:07:  54000000 
INFO  @ Thu, 13 Apr 2017 13:49:09:  55000000 
INFO  @ Thu, 13 Apr 2017 13:49:11:  56000000 
INFO  @ Thu, 13 Apr 2017 13:49:13:  57000000 
INFO  @ Thu, 13 Apr 2017 13:49:14:  58000000 
INFO  @ Thu, 13 Apr 2017 13:49:16:  59000000 
INFO  @ Thu, 13 Apr 2017 13:49:18:  60000000 
INFO  @ Thu, 13 Apr 2017 13:49:20:  61000000 
INFO  @ Thu, 13 Apr 2017 13:49:22:  62000000 
INFO  @ Thu, 13 Apr 2017 13:49:24:  63000000 
INFO  @ Thu, 13 Apr 2017 13:49:25:  64000000 
INFO  @ Thu, 13 Apr 2017 13:49:27:  65000000 
INFO  @ Thu, 13 Apr 2017 13:49:29:  66000000 
INFO  @ Thu, 13 Apr 2017 13:49:31:  67000000 
INFO  @ Thu, 13 Apr 2017 13:49:33:  68000000 
INFO  @ Thu, 13 Apr 2017 13:49:34:  69000000 
INFO  @ Thu, 13 Apr 2017 13:49:36:  70000000 
INFO  @ Thu, 13 Apr 2017 13:49:38:  71000000 
INFO  @ Thu, 13 Apr 2017 13:49:40:  72000000 
INFO  @ Thu, 13 Apr 2017 13:49:42:  73000000 
INFO  @ Thu, 13 Apr 2017 13:49:43:  74000000 
INFO  @ Thu, 13 Apr 2017 13:49:45:  75000000 
INFO  @ Thu, 13 Apr 2017 13:49:47:  76000000 
INFO  @ Thu, 13 Apr 2017 13:49:49:  77000000 
INFO  @ Thu, 13 Apr 2017 13:49:51:  78000000 
INFO  @ Thu, 13 Apr 2017 13:49:52:  79000000 
INFO  @ Thu, 13 Apr 2017 13:49:54:  80000000 
INFO  @ Thu, 13 Apr 2017 13:49:56:  81000000 
INFO  @ Thu, 13 Apr 2017 13:49:58:  82000000 
INFO  @ Thu, 13 Apr 2017 13:50:00:  83000000 
INFO  @ Thu, 13 Apr 2017 13:50:01:  84000000 
INFO  @ Thu, 13 Apr 2017 13:50:03:  85000000 
INFO  @ Thu, 13 Apr 2017 13:50:05:  86000000 
INFO  @ Thu, 13 Apr 2017 13:50:07:  87000000 
INFO  @ Thu, 13 Apr 2017 13:50:09:  88000000 
INFO  @ Thu, 13 Apr 2017 13:50:11:  89000000 
INFO  @ Thu, 13 Apr 2017 13:50:12:  90000000 
INFO  @ Thu, 13 Apr 2017 13:50:14:  91000000 
INFO  @ Thu, 13 Apr 2017 13:50:16:  92000000 
INFO  @ Thu, 13 Apr 2017 13:50:18:  93000000 
INFO  @ Thu, 13 Apr 2017 13:50:20:  94000000 
INFO  @ Thu, 13 Apr 2017 13:50:21:  95000000 
INFO  @ Thu, 13 Apr 2017 13:50:23:  96000000 
INFO  @ Thu, 13 Apr 2017 13:50:25:  97000000 
INFO  @ Thu, 13 Apr 2017 13:50:27:  98000000 
INFO  @ Thu, 13 Apr 2017 13:50:28:  99000000 
INFO  @ Thu, 13 Apr 2017 13:50:30: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:50:30: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:50:30: #1  total tags in treatment: 24587032 
INFO  @ Thu, 13 Apr 2017 13:50:30: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:50:30: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:50:30: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:50:30: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:50:30: #2 Use 195 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:50:30: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:50:30: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:50:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:58:17: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:58:17: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:58:17: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:58:17: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:58:17: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:08:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:09:03: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:09:06: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:09:07: Done! 
INFO  @ Thu, 13 Apr 2017 14:09:10: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:10:09: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:13:27: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:15:01: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:25:12: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:30:35: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:42:53: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:43:54: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:47:12: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:48:43: Values in your input bedGraph files will be multiplied by 24.587032 ... 
INFO  @ Thu, 13 Apr 2017 14:58:01: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 14:59:42: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:05:18: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'!

Num	14
ID	task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_23
Name	macs2 n/s rep1-pr1
Thread	thread_Root
PID	46857

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 13:46:11
End	2017-04-13 14:01:34
Elapsed	00:15:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 195 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
29345 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:46:35: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 195 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 13:46:35: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:46:35: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:46:37:  1000000 
INFO  @ Thu, 13 Apr 2017 13:46:39:  2000000 
INFO  @ Thu, 13 Apr 2017 13:46:40:  3000000 
INFO  @ Thu, 13 Apr 2017 13:46:42:  4000000 
INFO  @ Thu, 13 Apr 2017 13:46:44:  5000000 
INFO  @ Thu, 13 Apr 2017 13:46:45:  6000000 
INFO  @ Thu, 13 Apr 2017 13:46:47:  7000000 
INFO  @ Thu, 13 Apr 2017 13:46:48:  8000000 
INFO  @ Thu, 13 Apr 2017 13:46:50:  9000000 
INFO  @ Thu, 13 Apr 2017 13:46:51:  10000000 
INFO  @ Thu, 13 Apr 2017 13:46:53:  11000000 
INFO  @ Thu, 13 Apr 2017 13:46:55:  12000000 
INFO  @ Thu, 13 Apr 2017 13:46:56: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:46:58:  1000000 
INFO  @ Thu, 13 Apr 2017 13:46:59:  2000000 
INFO  @ Thu, 13 Apr 2017 13:47:01:  3000000 
INFO  @ Thu, 13 Apr 2017 13:47:02:  4000000 
INFO  @ Thu, 13 Apr 2017 13:47:03:  5000000 
INFO  @ Thu, 13 Apr 2017 13:47:05:  6000000 
INFO  @ Thu, 13 Apr 2017 13:47:06:  7000000 
INFO  @ Thu, 13 Apr 2017 13:47:08:  8000000 
INFO  @ Thu, 13 Apr 2017 13:47:09:  9000000 
INFO  @ Thu, 13 Apr 2017 13:47:10:  10000000 
INFO  @ Thu, 13 Apr 2017 13:47:12:  11000000 
INFO  @ Thu, 13 Apr 2017 13:47:13:  12000000 
INFO  @ Thu, 13 Apr 2017 13:47:15:  13000000 
INFO  @ Thu, 13 Apr 2017 13:47:16:  14000000 
INFO  @ Thu, 13 Apr 2017 13:47:18:  15000000 
INFO  @ Thu, 13 Apr 2017 13:47:19:  16000000 
INFO  @ Thu, 13 Apr 2017 13:47:20:  17000000 
INFO  @ Thu, 13 Apr 2017 13:47:22:  18000000 
INFO  @ Thu, 13 Apr 2017 13:47:23:  19000000 
INFO  @ Thu, 13 Apr 2017 13:47:25:  20000000 
INFO  @ Thu, 13 Apr 2017 13:47:26:  21000000 
INFO  @ Thu, 13 Apr 2017 13:47:28:  22000000 
INFO  @ Thu, 13 Apr 2017 13:47:29:  23000000 
INFO  @ Thu, 13 Apr 2017 13:47:30:  24000000 
INFO  @ Thu, 13 Apr 2017 13:47:32:  25000000 
INFO  @ Thu, 13 Apr 2017 13:47:33:  26000000 
INFO  @ Thu, 13 Apr 2017 13:47:35:  27000000 
INFO  @ Thu, 13 Apr 2017 13:47:36:  28000000 
INFO  @ Thu, 13 Apr 2017 13:47:37:  29000000 
INFO  @ Thu, 13 Apr 2017 13:47:39:  30000000 
INFO  @ Thu, 13 Apr 2017 13:47:40:  31000000 
INFO  @ Thu, 13 Apr 2017 13:47:42:  32000000 
INFO  @ Thu, 13 Apr 2017 13:47:43:  33000000 
INFO  @ Thu, 13 Apr 2017 13:47:45:  34000000 
INFO  @ Thu, 13 Apr 2017 13:47:46:  35000000 
INFO  @ Thu, 13 Apr 2017 13:47:48:  36000000 
INFO  @ Thu, 13 Apr 2017 13:47:49:  37000000 
INFO  @ Thu, 13 Apr 2017 13:47:51:  38000000 
INFO  @ Thu, 13 Apr 2017 13:47:52:  39000000 
INFO  @ Thu, 13 Apr 2017 13:47:53:  40000000 
INFO  @ Thu, 13 Apr 2017 13:47:55:  41000000 
INFO  @ Thu, 13 Apr 2017 13:47:56:  42000000 
INFO  @ Thu, 13 Apr 2017 13:47:58:  43000000 
INFO  @ Thu, 13 Apr 2017 13:47:59:  44000000 
INFO  @ Thu, 13 Apr 2017 13:48:01:  45000000 
INFO  @ Thu, 13 Apr 2017 13:48:02:  46000000 
INFO  @ Thu, 13 Apr 2017 13:48:04:  47000000 
INFO  @ Thu, 13 Apr 2017 13:48:05:  48000000 
INFO  @ Thu, 13 Apr 2017 13:48:06:  49000000 
INFO  @ Thu, 13 Apr 2017 13:48:08:  50000000 
INFO  @ Thu, 13 Apr 2017 13:48:09:  51000000 
INFO  @ Thu, 13 Apr 2017 13:48:11:  52000000 
INFO  @ Thu, 13 Apr 2017 13:48:12:  53000000 
INFO  @ Thu, 13 Apr 2017 13:48:13:  54000000 
INFO  @ Thu, 13 Apr 2017 13:48:15:  55000000 
INFO  @ Thu, 13 Apr 2017 13:48:16:  56000000 
INFO  @ Thu, 13 Apr 2017 13:48:18:  57000000 
INFO  @ Thu, 13 Apr 2017 13:48:19:  58000000 
INFO  @ Thu, 13 Apr 2017 13:48:21:  59000000 
INFO  @ Thu, 13 Apr 2017 13:48:22:  60000000 
INFO  @ Thu, 13 Apr 2017 13:48:24:  61000000 
INFO  @ Thu, 13 Apr 2017 13:48:25:  62000000 
INFO  @ Thu, 13 Apr 2017 13:48:27:  63000000 
INFO  @ Thu, 13 Apr 2017 13:48:28:  64000000 
INFO  @ Thu, 13 Apr 2017 13:48:29:  65000000 
INFO  @ Thu, 13 Apr 2017 13:48:31:  66000000 
INFO  @ Thu, 13 Apr 2017 13:48:32:  67000000 
INFO  @ Thu, 13 Apr 2017 13:48:34:  68000000 
INFO  @ Thu, 13 Apr 2017 13:48:35:  69000000 
INFO  @ Thu, 13 Apr 2017 13:48:36:  70000000 
INFO  @ Thu, 13 Apr 2017 13:48:38:  71000000 
INFO  @ Thu, 13 Apr 2017 13:48:39:  72000000 
INFO  @ Thu, 13 Apr 2017 13:48:41:  73000000 
INFO  @ Thu, 13 Apr 2017 13:48:42:  74000000 
INFO  @ Thu, 13 Apr 2017 13:48:44:  75000000 
INFO  @ Thu, 13 Apr 2017 13:48:46:  76000000 
INFO  @ Thu, 13 Apr 2017 13:48:47:  77000000 
INFO  @ Thu, 13 Apr 2017 13:48:48:  78000000 
INFO  @ Thu, 13 Apr 2017 13:48:50:  79000000 
INFO  @ Thu, 13 Apr 2017 13:48:51:  80000000 
INFO  @ Thu, 13 Apr 2017 13:48:53:  81000000 
INFO  @ Thu, 13 Apr 2017 13:48:54:  82000000 
INFO  @ Thu, 13 Apr 2017 13:48:55:  83000000 
INFO  @ Thu, 13 Apr 2017 13:48:57:  84000000 
INFO  @ Thu, 13 Apr 2017 13:48:58:  85000000 
INFO  @ Thu, 13 Apr 2017 13:49:00:  86000000 
INFO  @ Thu, 13 Apr 2017 13:49:01:  87000000 
INFO  @ Thu, 13 Apr 2017 13:49:03:  88000000 
INFO  @ Thu, 13 Apr 2017 13:49:04:  89000000 
INFO  @ Thu, 13 Apr 2017 13:49:06:  90000000 
INFO  @ Thu, 13 Apr 2017 13:49:07:  91000000 
INFO  @ Thu, 13 Apr 2017 13:49:09:  92000000 
INFO  @ Thu, 13 Apr 2017 13:49:10:  93000000 
INFO  @ Thu, 13 Apr 2017 13:49:11:  94000000 
INFO  @ Thu, 13 Apr 2017 13:49:13:  95000000 
INFO  @ Thu, 13 Apr 2017 13:49:14:  96000000 
INFO  @ Thu, 13 Apr 2017 13:49:16:  97000000 
INFO  @ Thu, 13 Apr 2017 13:49:17:  98000000 
INFO  @ Thu, 13 Apr 2017 13:49:18:  99000000 
INFO  @ Thu, 13 Apr 2017 13:49:20: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:49:20: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:49:20: #1  total tags in treatment: 12293516 
INFO  @ Thu, 13 Apr 2017 13:49:20: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:49:20: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:49:20: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:49:20: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:49:20: #2 Use 195 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:49:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:01:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:01:28: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:01:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:01:30: Done!

Num	15
ID	task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_24
Name	macs2 n/s rep1-pr2
Thread	thread_Root
PID	46866

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 14:01:37
End	2017-04-13 14:16:46
Elapsed	00:15:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 195 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
10931 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 14:02:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 195 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 14:02:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 14:02:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 14:02:03:  1000000 
INFO  @ Thu, 13 Apr 2017 14:02:05:  2000000 
INFO  @ Thu, 13 Apr 2017 14:02:07:  3000000 
INFO  @ Thu, 13 Apr 2017 14:02:08:  4000000 
INFO  @ Thu, 13 Apr 2017 14:02:10:  5000000 
INFO  @ Thu, 13 Apr 2017 14:02:11:  6000000 
INFO  @ Thu, 13 Apr 2017 14:02:13:  7000000 
INFO  @ Thu, 13 Apr 2017 14:02:15:  8000000 
INFO  @ Thu, 13 Apr 2017 14:02:16:  9000000 
INFO  @ Thu, 13 Apr 2017 14:02:18:  10000000 
INFO  @ Thu, 13 Apr 2017 14:02:19:  11000000 
INFO  @ Thu, 13 Apr 2017 14:02:21:  12000000 
INFO  @ Thu, 13 Apr 2017 14:02:22: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 14:02:23:  1000000 
INFO  @ Thu, 13 Apr 2017 14:02:24:  2000000 
INFO  @ Thu, 13 Apr 2017 14:02:26:  3000000 
INFO  @ Thu, 13 Apr 2017 14:02:27:  4000000 
INFO  @ Thu, 13 Apr 2017 14:02:29:  5000000 
INFO  @ Thu, 13 Apr 2017 14:02:30:  6000000 
INFO  @ Thu, 13 Apr 2017 14:02:32:  7000000 
INFO  @ Thu, 13 Apr 2017 14:02:33:  8000000 
INFO  @ Thu, 13 Apr 2017 14:02:34:  9000000 
INFO  @ Thu, 13 Apr 2017 14:02:36:  10000000 
INFO  @ Thu, 13 Apr 2017 14:02:37:  11000000 
INFO  @ Thu, 13 Apr 2017 14:02:39:  12000000 
INFO  @ Thu, 13 Apr 2017 14:02:40:  13000000 
INFO  @ Thu, 13 Apr 2017 14:02:41:  14000000 
INFO  @ Thu, 13 Apr 2017 14:02:43:  15000000 
INFO  @ Thu, 13 Apr 2017 14:02:44:  16000000 
INFO  @ Thu, 13 Apr 2017 14:02:46:  17000000 
INFO  @ Thu, 13 Apr 2017 14:02:47:  18000000 
INFO  @ Thu, 13 Apr 2017 14:02:48:  19000000 
INFO  @ Thu, 13 Apr 2017 14:02:50:  20000000 
INFO  @ Thu, 13 Apr 2017 14:02:51:  21000000 
INFO  @ Thu, 13 Apr 2017 14:02:53:  22000000 
INFO  @ Thu, 13 Apr 2017 14:02:54:  23000000 
INFO  @ Thu, 13 Apr 2017 14:02:55:  24000000 
INFO  @ Thu, 13 Apr 2017 14:02:57:  25000000 
INFO  @ Thu, 13 Apr 2017 14:02:58:  26000000 
INFO  @ Thu, 13 Apr 2017 14:03:00:  27000000 
INFO  @ Thu, 13 Apr 2017 14:03:01:  28000000 
INFO  @ Thu, 13 Apr 2017 14:03:03:  29000000 
INFO  @ Thu, 13 Apr 2017 14:03:04:  30000000 
INFO  @ Thu, 13 Apr 2017 14:03:05:  31000000 
INFO  @ Thu, 13 Apr 2017 14:03:07:  32000000 
INFO  @ Thu, 13 Apr 2017 14:03:08:  33000000 
INFO  @ Thu, 13 Apr 2017 14:03:10:  34000000 
INFO  @ Thu, 13 Apr 2017 14:03:11:  35000000 
INFO  @ Thu, 13 Apr 2017 14:03:12:  36000000 
INFO  @ Thu, 13 Apr 2017 14:03:14:  37000000 
INFO  @ Thu, 13 Apr 2017 14:03:15:  38000000 
INFO  @ Thu, 13 Apr 2017 14:03:17:  39000000 
INFO  @ Thu, 13 Apr 2017 14:03:18:  40000000 
INFO  @ Thu, 13 Apr 2017 14:03:19:  41000000 
INFO  @ Thu, 13 Apr 2017 14:03:21:  42000000 
INFO  @ Thu, 13 Apr 2017 14:03:22:  43000000 
INFO  @ Thu, 13 Apr 2017 14:03:24:  44000000 
INFO  @ Thu, 13 Apr 2017 14:03:25:  45000000 
INFO  @ Thu, 13 Apr 2017 14:03:26:  46000000 
INFO  @ Thu, 13 Apr 2017 14:03:28:  47000000 
INFO  @ Thu, 13 Apr 2017 14:03:29:  48000000 
INFO  @ Thu, 13 Apr 2017 14:03:31:  49000000 
INFO  @ Thu, 13 Apr 2017 14:03:32:  50000000 
INFO  @ Thu, 13 Apr 2017 14:03:33:  51000000 
INFO  @ Thu, 13 Apr 2017 14:03:35:  52000000 
INFO  @ Thu, 13 Apr 2017 14:03:36:  53000000 
INFO  @ Thu, 13 Apr 2017 14:03:38:  54000000 
INFO  @ Thu, 13 Apr 2017 14:03:39:  55000000 
INFO  @ Thu, 13 Apr 2017 14:03:40:  56000000 
INFO  @ Thu, 13 Apr 2017 14:03:42:  57000000 
INFO  @ Thu, 13 Apr 2017 14:03:43:  58000000 
INFO  @ Thu, 13 Apr 2017 14:03:45:  59000000 
INFO  @ Thu, 13 Apr 2017 14:03:46:  60000000 
INFO  @ Thu, 13 Apr 2017 14:03:47:  61000000 
INFO  @ Thu, 13 Apr 2017 14:03:49:  62000000 
INFO  @ Thu, 13 Apr 2017 14:03:50:  63000000 
INFO  @ Thu, 13 Apr 2017 14:03:52:  64000000 
INFO  @ Thu, 13 Apr 2017 14:03:53:  65000000 
INFO  @ Thu, 13 Apr 2017 14:03:54:  66000000 
INFO  @ Thu, 13 Apr 2017 14:03:56:  67000000 
INFO  @ Thu, 13 Apr 2017 14:03:57:  68000000 
INFO  @ Thu, 13 Apr 2017 14:03:59:  69000000 
INFO  @ Thu, 13 Apr 2017 14:04:00:  70000000 
INFO  @ Thu, 13 Apr 2017 14:04:01:  71000000 
INFO  @ Thu, 13 Apr 2017 14:04:03:  72000000 
INFO  @ Thu, 13 Apr 2017 14:04:04:  73000000 
INFO  @ Thu, 13 Apr 2017 14:04:06:  74000000 
INFO  @ Thu, 13 Apr 2017 14:04:07:  75000000 
INFO  @ Thu, 13 Apr 2017 14:04:09:  76000000 
INFO  @ Thu, 13 Apr 2017 14:04:10:  77000000 
INFO  @ Thu, 13 Apr 2017 14:04:11:  78000000 
INFO  @ Thu, 13 Apr 2017 14:04:13:  79000000 
INFO  @ Thu, 13 Apr 2017 14:04:14:  80000000 
INFO  @ Thu, 13 Apr 2017 14:04:16:  81000000 
INFO  @ Thu, 13 Apr 2017 14:04:17:  82000000 
INFO  @ Thu, 13 Apr 2017 14:04:18:  83000000 
INFO  @ Thu, 13 Apr 2017 14:04:20:  84000000 
INFO  @ Thu, 13 Apr 2017 14:04:21:  85000000 
INFO  @ Thu, 13 Apr 2017 14:04:23:  86000000 
INFO  @ Thu, 13 Apr 2017 14:04:24:  87000000 
INFO  @ Thu, 13 Apr 2017 14:04:25:  88000000 
INFO  @ Thu, 13 Apr 2017 14:04:27:  89000000 
INFO  @ Thu, 13 Apr 2017 14:04:28:  90000000 
INFO  @ Thu, 13 Apr 2017 14:04:30:  91000000 
INFO  @ Thu, 13 Apr 2017 14:04:31:  92000000 
INFO  @ Thu, 13 Apr 2017 14:04:32:  93000000 
INFO  @ Thu, 13 Apr 2017 14:04:34:  94000000 
INFO  @ Thu, 13 Apr 2017 14:04:35:  95000000 
INFO  @ Thu, 13 Apr 2017 14:04:37:  96000000 
INFO  @ Thu, 13 Apr 2017 14:04:38:  97000000 
INFO  @ Thu, 13 Apr 2017 14:04:39:  98000000 
INFO  @ Thu, 13 Apr 2017 14:04:41:  99000000 
INFO  @ Thu, 13 Apr 2017 14:04:42: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 14:04:42: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 14:04:42: #1  total tags in treatment: 12293516 
INFO  @ Thu, 13 Apr 2017 14:04:42: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 14:04:42: #1 finished! 
INFO  @ Thu, 13 Apr 2017 14:04:42: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 14:04:42: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 14:04:42: #2 Use 195 as fragment length 
INFO  @ Thu, 13 Apr 2017 14:04:42: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 14:04:42: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 14:04:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:09:37: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:09:37: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:09:37: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:09:37: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:09:37: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:16:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:16:41: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:16:42: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:16:43: Done!

Num	16
ID	task.callpeak_macs2.macs2_n_s_rep2.line_66.id_25
Name	macs2 n/s rep2
Thread	thread_Root
PID	46867

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 14:02:42
End	2017-04-13 15:16:08
Elapsed	01:13:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 225 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2 -o "ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2 -o "ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/signal/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
13181 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 14:03:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 225 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 14:03:01: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 14:03:01: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 14:03:03:  1000000 
INFO  @ Thu, 13 Apr 2017 14:03:04:  2000000 
INFO  @ Thu, 13 Apr 2017 14:03:06:  3000000 
INFO  @ Thu, 13 Apr 2017 14:03:07:  4000000 
INFO  @ Thu, 13 Apr 2017 14:03:09:  5000000 
INFO  @ Thu, 13 Apr 2017 14:03:11:  6000000 
INFO  @ Thu, 13 Apr 2017 14:03:12:  7000000 
INFO  @ Thu, 13 Apr 2017 14:03:14:  8000000 
INFO  @ Thu, 13 Apr 2017 14:03:15:  9000000 
INFO  @ Thu, 13 Apr 2017 14:03:17:  10000000 
INFO  @ Thu, 13 Apr 2017 14:03:19:  11000000 
INFO  @ Thu, 13 Apr 2017 14:03:20:  12000000 
INFO  @ Thu, 13 Apr 2017 14:03:22:  13000000 
INFO  @ Thu, 13 Apr 2017 14:03:23:  14000000 
INFO  @ Thu, 13 Apr 2017 14:03:25:  15000000 
INFO  @ Thu, 13 Apr 2017 14:03:27:  16000000 
INFO  @ Thu, 13 Apr 2017 14:03:28:  17000000 
INFO  @ Thu, 13 Apr 2017 14:03:30:  18000000 
INFO  @ Thu, 13 Apr 2017 14:03:31:  19000000 
INFO  @ Thu, 13 Apr 2017 14:03:33:  20000000 
INFO  @ Thu, 13 Apr 2017 14:03:35: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 14:03:37:  1000000 
INFO  @ Thu, 13 Apr 2017 14:03:38:  2000000 
INFO  @ Thu, 13 Apr 2017 14:03:39:  3000000 
INFO  @ Thu, 13 Apr 2017 14:03:41:  4000000 
INFO  @ Thu, 13 Apr 2017 14:03:42:  5000000 
INFO  @ Thu, 13 Apr 2017 14:03:44:  6000000 
INFO  @ Thu, 13 Apr 2017 14:03:45:  7000000 
INFO  @ Thu, 13 Apr 2017 14:03:47:  8000000 
INFO  @ Thu, 13 Apr 2017 14:03:48:  9000000 
INFO  @ Thu, 13 Apr 2017 14:03:50:  10000000 
INFO  @ Thu, 13 Apr 2017 14:03:51:  11000000 
INFO  @ Thu, 13 Apr 2017 14:03:53:  12000000 
INFO  @ Thu, 13 Apr 2017 14:03:54:  13000000 
INFO  @ Thu, 13 Apr 2017 14:03:56:  14000000 
INFO  @ Thu, 13 Apr 2017 14:03:57:  15000000 
INFO  @ Thu, 13 Apr 2017 14:03:59:  16000000 
INFO  @ Thu, 13 Apr 2017 14:04:00:  17000000 
INFO  @ Thu, 13 Apr 2017 14:04:02:  18000000 
INFO  @ Thu, 13 Apr 2017 14:04:03:  19000000 
INFO  @ Thu, 13 Apr 2017 14:04:05:  20000000 
INFO  @ Thu, 13 Apr 2017 14:04:06:  21000000 
INFO  @ Thu, 13 Apr 2017 14:04:08:  22000000 
INFO  @ Thu, 13 Apr 2017 14:04:09:  23000000 
INFO  @ Thu, 13 Apr 2017 14:04:10:  24000000 
INFO  @ Thu, 13 Apr 2017 14:04:12:  25000000 
INFO  @ Thu, 13 Apr 2017 14:04:13:  26000000 
INFO  @ Thu, 13 Apr 2017 14:04:15:  27000000 
INFO  @ Thu, 13 Apr 2017 14:04:16:  28000000 
INFO  @ Thu, 13 Apr 2017 14:04:18:  29000000 
INFO  @ Thu, 13 Apr 2017 14:04:19:  30000000 
INFO  @ Thu, 13 Apr 2017 14:04:21:  31000000 
INFO  @ Thu, 13 Apr 2017 14:04:22:  32000000 
INFO  @ Thu, 13 Apr 2017 14:04:24:  33000000 
INFO  @ Thu, 13 Apr 2017 14:04:25:  34000000 
INFO  @ Thu, 13 Apr 2017 14:04:27:  35000000 
INFO  @ Thu, 13 Apr 2017 14:04:28:  36000000 
INFO  @ Thu, 13 Apr 2017 14:04:30:  37000000 
INFO  @ Thu, 13 Apr 2017 14:04:31:  38000000 
INFO  @ Thu, 13 Apr 2017 14:04:33:  39000000 
INFO  @ Thu, 13 Apr 2017 14:04:34:  40000000 
INFO  @ Thu, 13 Apr 2017 14:04:35:  41000000 
INFO  @ Thu, 13 Apr 2017 14:04:37:  42000000 
INFO  @ Thu, 13 Apr 2017 14:04:38:  43000000 
INFO  @ Thu, 13 Apr 2017 14:04:40:  44000000 
INFO  @ Thu, 13 Apr 2017 14:04:41:  45000000 
INFO  @ Thu, 13 Apr 2017 14:04:43:  46000000 
INFO  @ Thu, 13 Apr 2017 14:04:44:  47000000 
INFO  @ Thu, 13 Apr 2017 14:04:46:  48000000 
INFO  @ Thu, 13 Apr 2017 14:04:47:  49000000 
INFO  @ Thu, 13 Apr 2017 14:04:48:  50000000 
INFO  @ Thu, 13 Apr 2017 14:04:50:  51000000 
INFO  @ Thu, 13 Apr 2017 14:04:51:  52000000 
INFO  @ Thu, 13 Apr 2017 14:04:53:  53000000 
INFO  @ Thu, 13 Apr 2017 14:04:54:  54000000 
INFO  @ Thu, 13 Apr 2017 14:04:56:  55000000 
INFO  @ Thu, 13 Apr 2017 14:04:57:  56000000 
INFO  @ Thu, 13 Apr 2017 14:04:59:  57000000 
INFO  @ Thu, 13 Apr 2017 14:05:00:  58000000 
INFO  @ Thu, 13 Apr 2017 14:05:01:  59000000 
INFO  @ Thu, 13 Apr 2017 14:05:03:  60000000 
INFO  @ Thu, 13 Apr 2017 14:05:05:  61000000 
INFO  @ Thu, 13 Apr 2017 14:05:06:  62000000 
INFO  @ Thu, 13 Apr 2017 14:05:08:  63000000 
INFO  @ Thu, 13 Apr 2017 14:05:09:  64000000 
INFO  @ Thu, 13 Apr 2017 14:05:10:  65000000 
INFO  @ Thu, 13 Apr 2017 14:05:12:  66000000 
INFO  @ Thu, 13 Apr 2017 14:05:13:  67000000 
INFO  @ Thu, 13 Apr 2017 14:05:15:  68000000 
INFO  @ Thu, 13 Apr 2017 14:05:16:  69000000 
INFO  @ Thu, 13 Apr 2017 14:05:18:  70000000 
INFO  @ Thu, 13 Apr 2017 14:05:19:  71000000 
INFO  @ Thu, 13 Apr 2017 14:05:20:  72000000 
INFO  @ Thu, 13 Apr 2017 14:05:22:  73000000 
INFO  @ Thu, 13 Apr 2017 14:05:23:  74000000 
INFO  @ Thu, 13 Apr 2017 14:05:25:  75000000 
INFO  @ Thu, 13 Apr 2017 14:05:26:  76000000 
INFO  @ Thu, 13 Apr 2017 14:05:28:  77000000 
INFO  @ Thu, 13 Apr 2017 14:05:29:  78000000 
INFO  @ Thu, 13 Apr 2017 14:05:31:  79000000 
INFO  @ Thu, 13 Apr 2017 14:05:32:  80000000 
INFO  @ Thu, 13 Apr 2017 14:05:34:  81000000 
INFO  @ Thu, 13 Apr 2017 14:05:35:  82000000 
INFO  @ Thu, 13 Apr 2017 14:05:37:  83000000 
INFO  @ Thu, 13 Apr 2017 14:05:38:  84000000 
INFO  @ Thu, 13 Apr 2017 14:05:40:  85000000 
INFO  @ Thu, 13 Apr 2017 14:05:41:  86000000 
INFO  @ Thu, 13 Apr 2017 14:05:42:  87000000 
INFO  @ Thu, 13 Apr 2017 14:05:44:  88000000 
INFO  @ Thu, 13 Apr 2017 14:05:45:  89000000 
INFO  @ Thu, 13 Apr 2017 14:05:47:  90000000 
INFO  @ Thu, 13 Apr 2017 14:05:48:  91000000 
INFO  @ Thu, 13 Apr 2017 14:05:50:  92000000 
INFO  @ Thu, 13 Apr 2017 14:05:51:  93000000 
INFO  @ Thu, 13 Apr 2017 14:05:53:  94000000 
INFO  @ Thu, 13 Apr 2017 14:05:54:  95000000 
INFO  @ Thu, 13 Apr 2017 14:05:56:  96000000 
INFO  @ Thu, 13 Apr 2017 14:05:57:  97000000 
INFO  @ Thu, 13 Apr 2017 14:05:58:  98000000 
INFO  @ Thu, 13 Apr 2017 14:06:00:  99000000 
INFO  @ Thu, 13 Apr 2017 14:06:01: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 14:06:01: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 14:06:01: #1  total tags in treatment: 20615486 
INFO  @ Thu, 13 Apr 2017 14:06:01: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 14:06:01: #1 finished! 
INFO  @ Thu, 13 Apr 2017 14:06:01: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 14:06:01: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 14:06:01: #2 Use 225 as fragment length 
INFO  @ Thu, 13 Apr 2017 14:06:01: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 14:06:01: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 14:06:01: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:13:01: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:13:01: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:13:01: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:13:01: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:13:01: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:22:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:22:54: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:22:55: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:22:55: Done! 
INFO  @ Thu, 13 Apr 2017 14:22:59: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:23:39: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:26:15: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:27:42: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:35:11: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:39:46: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:48:21: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:49:07: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:52:08: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:53:01: Values in your input bedGraph files will be multiplied by 20.615486 ... 
INFO  @ Thu, 13 Apr 2017 15:00:06: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 15:01:17: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:05:40: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'!

Num	17
ID	task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_26
Name	macs2 n/s rep2-pr1
Thread	thread_Root
PID	46869

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 14:09:12
End	2017-04-13 14:31:35
Elapsed	00:22:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 225 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
29512 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 14:09:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 225 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 14:09:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 14:09:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 14:09:35:  1000000 
INFO  @ Thu, 13 Apr 2017 14:09:37:  2000000 
INFO  @ Thu, 13 Apr 2017 14:09:39:  3000000 
INFO  @ Thu, 13 Apr 2017 14:09:41:  4000000 
INFO  @ Thu, 13 Apr 2017 14:09:43:  5000000 
INFO  @ Thu, 13 Apr 2017 14:09:45:  6000000 
INFO  @ Thu, 13 Apr 2017 14:09:47:  7000000 
INFO  @ Thu, 13 Apr 2017 14:09:50:  8000000 
INFO  @ Thu, 13 Apr 2017 14:09:52:  9000000 
INFO  @ Thu, 13 Apr 2017 14:09:54:  10000000 
INFO  @ Thu, 13 Apr 2017 14:09:55: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 14:09:57:  1000000 
INFO  @ Thu, 13 Apr 2017 14:09:59:  2000000 
INFO  @ Thu, 13 Apr 2017 14:10:01:  3000000 
INFO  @ Thu, 13 Apr 2017 14:10:03:  4000000 
INFO  @ Thu, 13 Apr 2017 14:10:05:  5000000 
INFO  @ Thu, 13 Apr 2017 14:10:06:  6000000 
INFO  @ Thu, 13 Apr 2017 14:10:08:  7000000 
INFO  @ Thu, 13 Apr 2017 14:10:10:  8000000 
INFO  @ Thu, 13 Apr 2017 14:10:12:  9000000 
INFO  @ Thu, 13 Apr 2017 14:10:14:  10000000 
INFO  @ Thu, 13 Apr 2017 14:10:16:  11000000 
INFO  @ Thu, 13 Apr 2017 14:10:18:  12000000 
INFO  @ Thu, 13 Apr 2017 14:10:20:  13000000 
INFO  @ Thu, 13 Apr 2017 14:10:22:  14000000 
INFO  @ Thu, 13 Apr 2017 14:10:24:  15000000 
INFO  @ Thu, 13 Apr 2017 14:10:25:  16000000 
INFO  @ Thu, 13 Apr 2017 14:10:27:  17000000 
INFO  @ Thu, 13 Apr 2017 14:10:29:  18000000 
INFO  @ Thu, 13 Apr 2017 14:10:31:  19000000 
INFO  @ Thu, 13 Apr 2017 14:10:33:  20000000 
INFO  @ Thu, 13 Apr 2017 14:10:35:  21000000 
INFO  @ Thu, 13 Apr 2017 14:10:37:  22000000 
INFO  @ Thu, 13 Apr 2017 14:10:39:  23000000 
INFO  @ Thu, 13 Apr 2017 14:10:41:  24000000 
INFO  @ Thu, 13 Apr 2017 14:10:43:  25000000 
INFO  @ Thu, 13 Apr 2017 14:10:44:  26000000 
INFO  @ Thu, 13 Apr 2017 14:10:46:  27000000 
INFO  @ Thu, 13 Apr 2017 14:10:48:  28000000 
INFO  @ Thu, 13 Apr 2017 14:10:50:  29000000 
INFO  @ Thu, 13 Apr 2017 14:10:52:  30000000 
INFO  @ Thu, 13 Apr 2017 14:10:54:  31000000 
INFO  @ Thu, 13 Apr 2017 14:10:56:  32000000 
INFO  @ Thu, 13 Apr 2017 14:10:58:  33000000 
INFO  @ Thu, 13 Apr 2017 14:11:00:  34000000 
INFO  @ Thu, 13 Apr 2017 14:11:02:  35000000 
INFO  @ Thu, 13 Apr 2017 14:11:03:  36000000 
INFO  @ Thu, 13 Apr 2017 14:11:05:  37000000 
INFO  @ Thu, 13 Apr 2017 14:11:07:  38000000 
INFO  @ Thu, 13 Apr 2017 14:11:09:  39000000 
INFO  @ Thu, 13 Apr 2017 14:11:11:  40000000 
INFO  @ Thu, 13 Apr 2017 14:11:13:  41000000 
INFO  @ Thu, 13 Apr 2017 14:11:15:  42000000 
INFO  @ Thu, 13 Apr 2017 14:11:17:  43000000 
INFO  @ Thu, 13 Apr 2017 14:11:19:  44000000 
INFO  @ Thu, 13 Apr 2017 14:11:21:  45000000 
INFO  @ Thu, 13 Apr 2017 14:11:23:  46000000 
INFO  @ Thu, 13 Apr 2017 14:11:24:  47000000 
INFO  @ Thu, 13 Apr 2017 14:11:26:  48000000 
INFO  @ Thu, 13 Apr 2017 14:11:28:  49000000 
INFO  @ Thu, 13 Apr 2017 14:11:30:  50000000 
INFO  @ Thu, 13 Apr 2017 14:11:32:  51000000 
INFO  @ Thu, 13 Apr 2017 14:11:34:  52000000 
INFO  @ Thu, 13 Apr 2017 14:11:36:  53000000 
INFO  @ Thu, 13 Apr 2017 14:11:38:  54000000 
INFO  @ Thu, 13 Apr 2017 14:11:40:  55000000 
INFO  @ Thu, 13 Apr 2017 14:11:42:  56000000 
INFO  @ Thu, 13 Apr 2017 14:11:44:  57000000 
INFO  @ Thu, 13 Apr 2017 14:11:45:  58000000 
INFO  @ Thu, 13 Apr 2017 14:11:47:  59000000 
INFO  @ Thu, 13 Apr 2017 14:11:49:  60000000 
INFO  @ Thu, 13 Apr 2017 14:11:51:  61000000 
INFO  @ Thu, 13 Apr 2017 14:11:53:  62000000 
INFO  @ Thu, 13 Apr 2017 14:11:55:  63000000 
INFO  @ Thu, 13 Apr 2017 14:11:57:  64000000 
INFO  @ Thu, 13 Apr 2017 14:11:59:  65000000 
INFO  @ Thu, 13 Apr 2017 14:12:01:  66000000 
INFO  @ Thu, 13 Apr 2017 14:12:03:  67000000 
INFO  @ Thu, 13 Apr 2017 14:12:05:  68000000 
INFO  @ Thu, 13 Apr 2017 14:12:07:  69000000 
INFO  @ Thu, 13 Apr 2017 14:12:09:  70000000 
INFO  @ Thu, 13 Apr 2017 14:12:11:  71000000 
INFO  @ Thu, 13 Apr 2017 14:12:13:  72000000 
INFO  @ Thu, 13 Apr 2017 14:12:15:  73000000 
INFO  @ Thu, 13 Apr 2017 14:12:17:  74000000 
INFO  @ Thu, 13 Apr 2017 14:12:19:  75000000 
INFO  @ Thu, 13 Apr 2017 14:12:21:  76000000 
INFO  @ Thu, 13 Apr 2017 14:12:23:  77000000 
INFO  @ Thu, 13 Apr 2017 14:12:25:  78000000 
INFO  @ Thu, 13 Apr 2017 14:12:27:  79000000 
INFO  @ Thu, 13 Apr 2017 14:12:29:  80000000 
INFO  @ Thu, 13 Apr 2017 14:12:31:  81000000 
INFO  @ Thu, 13 Apr 2017 14:12:33:  82000000 
INFO  @ Thu, 13 Apr 2017 14:12:35:  83000000 
INFO  @ Thu, 13 Apr 2017 14:12:37:  84000000 
INFO  @ Thu, 13 Apr 2017 14:12:39:  85000000 
INFO  @ Thu, 13 Apr 2017 14:12:41:  86000000 
INFO  @ Thu, 13 Apr 2017 14:12:43:  87000000 
INFO  @ Thu, 13 Apr 2017 14:12:45:  88000000 
INFO  @ Thu, 13 Apr 2017 14:12:47:  89000000 
INFO  @ Thu, 13 Apr 2017 14:12:49:  90000000 
INFO  @ Thu, 13 Apr 2017 14:12:51:  91000000 
INFO  @ Thu, 13 Apr 2017 14:12:53:  92000000 
INFO  @ Thu, 13 Apr 2017 14:12:55:  93000000 
INFO  @ Thu, 13 Apr 2017 14:12:57:  94000000 
INFO  @ Thu, 13 Apr 2017 14:12:59:  95000000 
INFO  @ Thu, 13 Apr 2017 14:13:01:  96000000 
INFO  @ Thu, 13 Apr 2017 14:13:03:  97000000 
INFO  @ Thu, 13 Apr 2017 14:13:05:  98000000 
INFO  @ Thu, 13 Apr 2017 14:13:07:  99000000 
INFO  @ Thu, 13 Apr 2017 14:13:09: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 14:13:09: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 14:13:09: #1  total tags in treatment: 10307744 
INFO  @ Thu, 13 Apr 2017 14:13:09: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 14:13:09: #1 finished! 
INFO  @ Thu, 13 Apr 2017 14:13:09: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 14:13:09: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 14:13:09: #2 Use 225 as fragment length 
INFO  @ Thu, 13 Apr 2017 14:13:09: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 14:13:09: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 14:13:09: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:21:50: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:21:50: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:21:50: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:21:50: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:21:50: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:31:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:31:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:31:28: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:31:30: Done!

Num	18
ID	task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_27
Name	macs2 n/s rep2-pr2
Thread	thread_Root
PID	46871

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 14:16:49
End	2017-04-13 14:31:33
Elapsed	00:14:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies

 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 225 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
44376 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 14:17:03: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 225 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 13 Apr 2017 14:17:03: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 14:17:03: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 14:17:05:  1000000 
INFO  @ Thu, 13 Apr 2017 14:17:06:  2000000 
INFO  @ Thu, 13 Apr 2017 14:17:08:  3000000 
INFO  @ Thu, 13 Apr 2017 14:17:09:  4000000 
INFO  @ Thu, 13 Apr 2017 14:17:11:  5000000 
INFO  @ Thu, 13 Apr 2017 14:17:12:  6000000 
INFO  @ Thu, 13 Apr 2017 14:17:14:  7000000 
INFO  @ Thu, 13 Apr 2017 14:17:15:  8000000 
INFO  @ Thu, 13 Apr 2017 14:17:17:  9000000 
INFO  @ Thu, 13 Apr 2017 14:17:18:  10000000 
INFO  @ Thu, 13 Apr 2017 14:17:19: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 14:17:21:  1000000 
INFO  @ Thu, 13 Apr 2017 14:17:22:  2000000 
INFO  @ Thu, 13 Apr 2017 14:17:24:  3000000 
INFO  @ Thu, 13 Apr 2017 14:17:25:  4000000 
INFO  @ Thu, 13 Apr 2017 14:17:26:  5000000 
INFO  @ Thu, 13 Apr 2017 14:17:28:  6000000 
INFO  @ Thu, 13 Apr 2017 14:17:29:  7000000 
INFO  @ Thu, 13 Apr 2017 14:17:31:  8000000 
INFO  @ Thu, 13 Apr 2017 14:17:32:  9000000 
INFO  @ Thu, 13 Apr 2017 14:17:33:  10000000 
INFO  @ Thu, 13 Apr 2017 14:17:35:  11000000 
INFO  @ Thu, 13 Apr 2017 14:17:36:  12000000 
INFO  @ Thu, 13 Apr 2017 14:17:38:  13000000 
INFO  @ Thu, 13 Apr 2017 14:17:39:  14000000 
INFO  @ Thu, 13 Apr 2017 14:17:40:  15000000 
INFO  @ Thu, 13 Apr 2017 14:17:42:  16000000 
INFO  @ Thu, 13 Apr 2017 14:17:43:  17000000 
INFO  @ Thu, 13 Apr 2017 14:17:45:  18000000 
INFO  @ Thu, 13 Apr 2017 14:17:46:  19000000 
INFO  @ Thu, 13 Apr 2017 14:17:47:  20000000 
INFO  @ Thu, 13 Apr 2017 14:17:49:  21000000 
INFO  @ Thu, 13 Apr 2017 14:17:50:  22000000 
INFO  @ Thu, 13 Apr 2017 14:17:51:  23000000 
INFO  @ Thu, 13 Apr 2017 14:17:53:  24000000 
INFO  @ Thu, 13 Apr 2017 14:17:54:  25000000 
INFO  @ Thu, 13 Apr 2017 14:17:56:  26000000 
INFO  @ Thu, 13 Apr 2017 14:17:57:  27000000 
INFO  @ Thu, 13 Apr 2017 14:17:58:  28000000 
INFO  @ Thu, 13 Apr 2017 14:18:00:  29000000 
INFO  @ Thu, 13 Apr 2017 14:18:01:  30000000 
INFO  @ Thu, 13 Apr 2017 14:18:03:  31000000 
INFO  @ Thu, 13 Apr 2017 14:18:04:  32000000 
INFO  @ Thu, 13 Apr 2017 14:18:05:  33000000 
INFO  @ Thu, 13 Apr 2017 14:18:07:  34000000 
INFO  @ Thu, 13 Apr 2017 14:18:08:  35000000 
INFO  @ Thu, 13 Apr 2017 14:18:10:  36000000 
INFO  @ Thu, 13 Apr 2017 14:18:11:  37000000 
INFO  @ Thu, 13 Apr 2017 14:18:12:  38000000 
INFO  @ Thu, 13 Apr 2017 14:18:14:  39000000 
INFO  @ Thu, 13 Apr 2017 14:18:15:  40000000 
INFO  @ Thu, 13 Apr 2017 14:18:17:  41000000 
INFO  @ Thu, 13 Apr 2017 14:18:18:  42000000 
INFO  @ Thu, 13 Apr 2017 14:18:19:  43000000 
INFO  @ Thu, 13 Apr 2017 14:18:21:  44000000 
INFO  @ Thu, 13 Apr 2017 14:18:22:  45000000 
INFO  @ Thu, 13 Apr 2017 14:18:24:  46000000 
INFO  @ Thu, 13 Apr 2017 14:18:25:  47000000 
INFO  @ Thu, 13 Apr 2017 14:18:27:  48000000 
INFO  @ Thu, 13 Apr 2017 14:18:28:  49000000 
INFO  @ Thu, 13 Apr 2017 14:18:29:  50000000 
INFO  @ Thu, 13 Apr 2017 14:18:31:  51000000 
INFO  @ Thu, 13 Apr 2017 14:18:32:  52000000 
INFO  @ Thu, 13 Apr 2017 14:18:34:  53000000 
INFO  @ Thu, 13 Apr 2017 14:18:35:  54000000 
INFO  @ Thu, 13 Apr 2017 14:18:36:  55000000 
INFO  @ Thu, 13 Apr 2017 14:18:38:  56000000 
INFO  @ Thu, 13 Apr 2017 14:18:39:  57000000 
INFO  @ Thu, 13 Apr 2017 14:18:41:  58000000 
INFO  @ Thu, 13 Apr 2017 14:18:42:  59000000 
INFO  @ Thu, 13 Apr 2017 14:18:43:  60000000 
INFO  @ Thu, 13 Apr 2017 14:18:45:  61000000 
INFO  @ Thu, 13 Apr 2017 14:18:46:  62000000 
INFO  @ Thu, 13 Apr 2017 14:18:48:  63000000 
INFO  @ Thu, 13 Apr 2017 14:18:49:  64000000 
INFO  @ Thu, 13 Apr 2017 14:18:50:  65000000 
INFO  @ Thu, 13 Apr 2017 14:18:52:  66000000 
INFO  @ Thu, 13 Apr 2017 14:18:53:  67000000 
INFO  @ Thu, 13 Apr 2017 14:18:55:  68000000 
INFO  @ Thu, 13 Apr 2017 14:18:56:  69000000 
INFO  @ Thu, 13 Apr 2017 14:18:57:  70000000 
INFO  @ Thu, 13 Apr 2017 14:18:59:  71000000 
INFO  @ Thu, 13 Apr 2017 14:19:00:  72000000 
INFO  @ Thu, 13 Apr 2017 14:19:02:  73000000 
INFO  @ Thu, 13 Apr 2017 14:19:03:  74000000 
INFO  @ Thu, 13 Apr 2017 14:19:04:  75000000 
INFO  @ Thu, 13 Apr 2017 14:19:06:  76000000 
INFO  @ Thu, 13 Apr 2017 14:19:07:  77000000 
INFO  @ Thu, 13 Apr 2017 14:19:09:  78000000 
INFO  @ Thu, 13 Apr 2017 14:19:10:  79000000 
INFO  @ Thu, 13 Apr 2017 14:19:11:  80000000 
INFO  @ Thu, 13 Apr 2017 14:19:13:  81000000 
INFO  @ Thu, 13 Apr 2017 14:19:14:  82000000 
INFO  @ Thu, 13 Apr 2017 14:19:16:  83000000 
INFO  @ Thu, 13 Apr 2017 14:19:17:  84000000 
INFO  @ Thu, 13 Apr 2017 14:19:18:  85000000 
INFO  @ Thu, 13 Apr 2017 14:19:20:  86000000 
INFO  @ Thu, 13 Apr 2017 14:19:21:  87000000 
INFO  @ Thu, 13 Apr 2017 14:19:23:  88000000 
INFO  @ Thu, 13 Apr 2017 14:19:24:  89000000 
INFO  @ Thu, 13 Apr 2017 14:19:26:  90000000 
INFO  @ Thu, 13 Apr 2017 14:19:27:  91000000 
INFO  @ Thu, 13 Apr 2017 14:19:28:  92000000 
INFO  @ Thu, 13 Apr 2017 14:19:30:  93000000 
INFO  @ Thu, 13 Apr 2017 14:19:31:  94000000 
INFO  @ Thu, 13 Apr 2017 14:19:33:  95000000 
INFO  @ Thu, 13 Apr 2017 14:19:34:  96000000 
INFO  @ Thu, 13 Apr 2017 14:19:35:  97000000 
INFO  @ Thu, 13 Apr 2017 14:19:37:  98000000 
INFO  @ Thu, 13 Apr 2017 14:19:38:  99000000 
INFO  @ Thu, 13 Apr 2017 14:19:39: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 14:19:39: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 14:19:39: #1  total tags in treatment: 10307742 
INFO  @ Thu, 13 Apr 2017 14:19:39: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 14:19:39: #1 finished! 
INFO  @ Thu, 13 Apr 2017 14:19:39: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 14:19:39: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 14:19:39: #2 Use 225 as fragment length 
INFO  @ Thu, 13 Apr 2017 14:19:39: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 14:19:39: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 14:19:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:24:20: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:24:20: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:24:20: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:24:20: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:24:20: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:31:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:31:28: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:31:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:31:29: Done!

Num	19
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_28
Name	naive_overlap
Thread	thread_Root
PID	46897

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:20:45
End	2017-04-13 15:22:00
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 145

 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 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.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 -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.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 -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 156

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
53466 (process ID) old priority 0, new priority 19
Waiting for 52 seconds.

Num	20
ID	task.callpeak_idr.idr2_rep1_rep2.line_74.id_29
Name	idr2 rep1-rep2
Thread	thread_Root
PID	46898

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:22:02
End	2017-04-13 15:27:34
Elapsed	00:05:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
57049 (process ID) old priority 0, new priority 19

Num	21
ID	task.callpeak_idr.idr2_rep1_pr.line_74.id_30
Name	idr2 rep1-pr
Thread	thread_Root
PID	46899

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:22:03
End	2017-04-13 15:28:13
Elapsed	00:06:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_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 -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
5562 (process ID) old priority 0, new priority 19

Num	22
ID	task.callpeak_idr.idr2_rep2_pr.line_74.id_31
Name	idr2 rep2-pr
Thread	thread_Root
PID	46900

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:22:04
End	2017-04-13 15:24:41
Elapsed	00:02:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-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 -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
57050 (process ID) old priority 0, new priority 19

Num	23
ID	task.callpeak_idr.idr2_ppr.line_74.id_32
Name	idr2 ppr
Thread	thread_Root
PID	46901

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:22:05
End	2017-04-13 15:30:15
Elapsed	00:08:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.log.txt /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.log.txt

# SYS command. line 82

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 85

 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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
5563 (process ID) old priority 0, new priority 19

Num	24
ID	task.sys.copy_file.line_131.id_41
Name	copy file
Thread	thread_Root
PID	25861

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:16
End	2017-04-13 15:30:16
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	25
ID	task.sys.copy_file.line_131.id_42
Name	copy file
Thread	thread_Root
PID	25866

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:16
End	2017-04-13 15:30:16
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	26
ID	task.sys.copy_file.line_131.id_43
Name	copy file
Thread	thread_Root
PID	25874

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:16
End	2017-04-13 15:30:16
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	27
ID	task.sys.copy_file.line_131.id_44
Name	copy file
Thread	thread_Root
PID	25889

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:16
End	2017-04-13 15:30:16
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	28
ID	task.callpeak_idr.idr_final_qc.line_283.id_45
Name	idr final qc
Thread	thread_Root
PID	46902

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:18
End	2017-04-13 15:31:30
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/EGR2_MACS2_IDR_final.qc
Dependencies

 
# SYS command. line 285

 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 287

 echo -e "Nt\tN1	N2	""Np\tN_opt\tN_consv\topt_set\tconsv_set\trescue_ratio\tself_consistency_ratio\treproducibility_test" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/EGR2_MACS2_IDR_final.qc

# SYS command. line 288

 echo -e "39100\t30688	21156	""40951\t40951\t39100\tpooled_pseudo_rep\trep1-rep2\t1.0473401534526854\t1.4505577613915674\tpass" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/EGR2_MACS2_IDR_final.qc

# SYS command. line 290

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
7963 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

Num	29
ID	task.callpeak_idr.FRiP_rep1_pr.line_120.id_46
Name	FRiP rep1-pr
Thread	thread_Root
PID	46903

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:20
End	2017-04-13 15:31:30
Elapsed	00:01:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 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 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -98 -r 98 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
26243 (process ID) old priority 0, new priority 19
Waiting for 1 seconds.

Num	30
ID	task.callpeak_idr.FRiP_rep2_pr.line_120.id_47
Name	FRiP rep2-pr
Thread	thread_Root
PID	46904

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:21
End	2017-04-13 15:31:46
Elapsed	00:01:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 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 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -113 -r 113 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8099 (process ID) old priority 0, new priority 19

Num	31
ID	task.callpeak_idr.FRiP_ppr.line_120.id_48
Name	FRiP ppr
Thread	thread_Root
PID	46905

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:21
End	2017-04-13 15:32:38
Elapsed	00:02:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 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 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -105 -r 105 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/EGR2_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
27342 (process ID) old priority 0, new priority 19

Num	32
ID	task.callpeak_idr.FRiP_rep1_rep2.line_120.id_49
Name	FRiP rep1-rep2
Thread	thread_Root
PID	46906

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:30:23
End	2017-04-13 15:32:59
Elapsed	00:02:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 121

 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 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -105 -r 105 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/EGR2_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8098 (process ID) old priority 0, new priority 19

Num	33
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_50
Name	blacklist_filter peak_pooled
Thread	thread_Root
PID	35682

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:33:01
End	2017-04-13 15:34:08
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 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 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
35686 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

Num	34
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_51
Name	blacklist_filter peak 1
Thread	thread_Root
PID	35769

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:33:02
End	2017-04-13 15:34:09
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 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 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
35774 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

Num	35
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_52
Name	blacklist_filter peak 2
Thread	thread_Root
PID	35858

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:33:02
End	2017-04-13 15:34:11
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 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 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
35863 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

Num	36
ID	task.report.peak2hammock.line_361.id_55
Name	peak2hammock
Thread	thread_Root
PID	39868

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:34:12
End	2017-04-13 15:34:21
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 363

 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 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
39873 (process ID) old priority 0, new priority 19

Num	37
ID	task.report.peak2hammock.line_361.id_56
Name	peak2hammock
Thread	thread_Root
PID	40540

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:34:22
End	2017-04-13 15:34:31
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 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 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/optimal_set/EGR2_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
40544 (process ID) old priority 0, new priority 19

Num	38
ID	task.report.peak2hammock.line_361.id_57
Name	peak2hammock
Thread	thread_Root
PID	41250

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:34:32
End	2017-04-13 15:34:41
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 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 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/conservative_set/EGR2_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
41254 (process ID) old priority 0, new priority 19

Num	39
ID	task.report.peak2hammock.line_361.id_58
Name	peak2hammock
Thread	thread_Root
PID	41726

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:34:42
End	2017-04-13 15:34:51
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 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 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/EGR2_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
41730 (process ID) old priority 0, new priority 19

Num	40
ID	task.report.peak2hammock.line_361.id_59
Name	peak2hammock
Thread	thread_Root
PID	42369

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:34:52
End	2017-04-13 15:35:01
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 363

 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 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/EGR2_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
42373 (process ID) old priority 0, new priority 19

Num	41
ID	task.graphviz.report.line_97.id_60
Name	report
Thread	thread_Root
PID	43010

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:35:02
End	2017-04-13 15:35:10
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 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 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/report/EGR2_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/report/EGR2_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/report/EGR2_MACS2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
43014 (process ID) old priority 0, new priority 19

Num	42
ID	task.report.pdf2png.line_328.id_61
Name	pdf2png
Thread	thread_Root
PID	43094

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:35:02
End	2017-04-13 15:35:10
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.plot.png
Dependencies

 
# SYS command. line 329

 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 330

 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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep1/ENCFF888DOH.15M.cc.plot.pdf

   
--------------------Stdout--------------------
43105 (process ID) old priority 0, new priority 19

Num	43
ID	task.report.pdf2png.line_328.id_62
Name	pdf2png
Thread	thread_Root
PID	43096

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 15:35:02
End	2017-04-13 15:35:10
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep2/ENCFF234ALA.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep2/ENCFF234ALA.15M.cc.plot.png
Dependencies

 
# SYS command. line 329

 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 330

 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/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep2/ENCFF234ALA.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/qc/rep2/ENCFF234ALA.15M.cc.plot.pdf

   
--------------------Stdout--------------------
43104 (process ID) old priority 0, new priority 19

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, EGR2_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/EGR2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $]
bool	canFail	false
string	CPATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
string	EVENT_NOEPOLL	1
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_CCx82k
string	LANG	en_US.UTF-8
string	LIBRARY_PATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/EGR2_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/EGR2_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	44250.EGR2_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

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope