Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170407_180225_971
Start time	2017-04-07 18:02:25
Run time	3 days 08:32:11.225
Tasks executed	33
Tasks failed	9
Tasks failed names	macs2 n/s rep2-pr1 macs2 n/s rep1 macs2 n/s pooled_rep macs2 n/s rep1-pr1 macs2 n/s rep2 macs2 n/s ppr1 macs2 n/s ppr2 macs2 n/s rep2-pr2 macs2 n/s rep1-pr2
Arguments*	[-title, ZBTB17_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB17_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, $]
System*	sge
Cpus*	-1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170407_180225_971/task.postalign_bed.pool_tag_pooled_rep.line_436.id_22 chipseq.bds.20170407_180225_971/task.postalign_bed.pool_tag_ppr1.line_436.id_23 chipseq.bds.20170407_180225_971/task.postalign_bed.pool_tag_ppr2.line_436.id_24 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_pooled_rep.line_59.id_25 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_26 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_ppr1.line_59.id_27 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_ppr2.line_59.id_28 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_29 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_30 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_rep1.line_59.id_31 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_32 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_rep1_pr1.line_59.id_33 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_rep1_pr2.line_59.id_34 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_35 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_36 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_rep2.line_59.id_37 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_38 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_rep2_pr1.line_59.id_39 chipseq.bds.20170407_180225_971/task.callpeak_spp.spp_rep2_pr2.line_59.id_40 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_41 chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_42
thread_41	thread_Root	chipseq.bds.20170407_180225_971_parallel_41/task.postalign_bam.nmsrt_bam_rep1.line_495.id_10 chipseq.bds.20170407_180225_971_parallel_41/task.postalign_bam.bam_to_bedpe_rep1.line_602.id_12 chipseq.bds.20170407_180225_971_parallel_41/task.postalign_bam.bedpe_to_tag_rep1.line_640.id_13 chipseq.bds.20170407_180225_971_parallel_41/task.postalign_bed.subsample_bedpe2tag_rep1.line_115.id_14 chipseq.bds.20170407_180225_971_parallel_41/task.postalign_bed.spr_PE_rep1.line_299.id_15 chipseq.bds.20170407_180225_971_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_17
thread_42	thread_Root	chipseq.bds.20170407_180225_971_parallel_42/task.postalign_bam.nmsrt_bam_rep2.line_495.id_11 chipseq.bds.20170407_180225_971_parallel_42/task.postalign_bam.bam_to_bedpe_rep2.line_602.id_16 chipseq.bds.20170407_180225_971_parallel_42/task.postalign_bam.bedpe_to_tag_rep2.line_640.id_18 chipseq.bds.20170407_180225_971_parallel_42/task.postalign_bed.subsample_bedpe2tag_rep2.line_115.id_19 chipseq.bds.20170407_180225_971_parallel_42/task.postalign_bed.spr_PE_rep2.line_299.id_20 chipseq.bds.20170407_180225_971_parallel_42/task.postalign_bed.xcor_rep2.line_212.id_21
thread_43	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.postalign_bam.nmsrt_bam_rep1.line_495.id_10
Name	nmsrt_bam rep1
Thread	thread_41
PID	46377

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

Start	2017-04-07 18:02:29
End	2017-04-07 18:35:23
Elapsed	00:32:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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--------------------
13506 (process ID) old priority 0, new priority 19

Num	2
ID	task.postalign_bam.nmsrt_bam_rep2.line_495.id_11
Name	nmsrt_bam rep2
Thread	thread_42
PID	46378

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

Start	2017-04-07 18:02:29
End	2017-04-07 18:41:13
Elapsed	00:38:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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--------------------
35687 (process ID) old priority 0, new priority 19

Num	3
ID	task.postalign_bam.bam_to_bedpe_rep1.line_602.id_12
Name	bam_to_bedpe rep1
Thread	thread_41
PID	46420

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

Start	2017-04-07 18:35:24
End	2017-04-07 18:38:35
Elapsed	00:03:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.nmsrt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.nmsrt.bam | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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--------------------
50066 (process ID) old priority 0, new priority 19

Num	4
ID	task.postalign_bam.bedpe_to_tag_rep1.line_640.id_13
Name	bedpe_to_tag rep1
Thread	thread_41
PID	46424

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

Start	2017-04-07 18:38:36
End	2017-04-07 18:40:19
Elapsed	00:01:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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--------------------
51438 (process ID) old priority 0, new priority 19

Num	5
ID	task.postalign_bed.subsample_bedpe2tag_rep1.line_115.id_14
Name	subsample_bedpe2tag rep1
Thread	thread_41
PID	46426

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

Start	2017-04-07 18:40:20
End	2017-04-07 18:41:30
Elapsed	00:01:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bedpe.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bedpe.gz | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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--------------------
52028 (process ID) old priority 0, new priority 19
Waiting for 8 seconds.

Num	6
ID	task.postalign_bed.spr_PE_rep1.line_299.id_15
Name	spr_PE rep1
Thread	thread_41
PID	46427

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

Start	2017-04-07 18:40:21
End	2017-04-07 18:42:55
Elapsed	00:02:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bedpe.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bedpe.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.  

# 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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.00" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz

# SYS command. line 314

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.01" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.gz

# SYS command. line 317

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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--------------------
44822 (process ID) old priority 0, new priority 19

Num	7
ID	task.postalign_bam.bam_to_bedpe_rep2.line_602.id_16
Name	bam_to_bedpe rep2
Thread	thread_42
PID	46428

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

Start	2017-04-07 18:41:14
End	2017-04-07 18:45:55
Elapsed	00:04:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.nmsrt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.nmsrt.bam | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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--------------------
52443 (process ID) old priority 0, new priority 19

Num	8
ID	task.postalign_bed.xcor_rep1.line_212.id_17
Name	xcor rep1
Thread	thread_41
PID	46430

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

Start	2017-04-07 18:42:56
End	2017-04-07 18:53:47
Elapsed	00:10:51
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.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--------------------
13466 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_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/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.15M.tagAlign.gz 
opened /tmp/46430.1.q/RtmptqhMfV/ENCFF057NJA.15M.tagAlign360712433052
done. read 15000000 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1803294 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.213303212112559,0.213238360586853,0.192751092772993 
Top 3 estimates for fragment length 265,275,655 
Window half size 690 
Phantom peak location 105 
Phantom peak Correlation 0.204199 
Normalized Strand cross-correlation coefficient (NSC) 1.182853 
Relative Strand cross-correlation Coefficient (RSC) 1.381415 
Phantom Peak Quality Tag 1 
null device 
          1 

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

Num	9
ID	task.postalign_bam.bedpe_to_tag_rep2.line_640.id_18
Name	bedpe_to_tag rep2
Thread	thread_42
PID	46434

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

Start	2017-04-07 18:45:56
End	2017-04-07 18:48:01
Elapsed	00:02:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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--------------------
49062 (process ID) old priority 0, new priority 19

Num	10
ID	task.postalign_bed.subsample_bedpe2tag_rep2.line_115.id_19
Name	subsample_bedpe2tag rep2
Thread	thread_42
PID	46436

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

Start	2017-04-07 18:48:03
End	2017-04-07 18:49:21
Elapsed	00:01:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bedpe.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bedpe.gz | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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--------------------
54938 (process ID) old priority 0, new priority 19

Num	11
ID	task.postalign_bed.spr_PE_rep2.line_299.id_20
Name	spr_PE rep2
Thread	thread_42
PID	46437

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

Start	2017-04-07 18:48:04
End	2017-04-07 18:51:04
Elapsed	00:03:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bedpe.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bedpe.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.  

# 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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.00" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz

# SYS command. line 314

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.01" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.gz

# SYS command. line 317

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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--------------------
2227 (process ID) old priority 0, new priority 19

Num	12
ID	task.postalign_bed.xcor_rep2.line_212.id_21
Name	xcor rep2
Thread	thread_42
PID	46438

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

Start	2017-04-07 18:51:05
End	2017-04-07 19:02:13
Elapsed	00:11:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.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--------------------
30399 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.15M.tagAlign.gz 
opened /tmp/46438.1.q/RtmpfnKuBV/ENCFF078YAS.15M.tagAlign77ef1ad37c2
done. read 15000000 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1791742 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.212565948653747 
Top 3 estimates for fragment length 245 
Window half size 635 
Phantom peak location 105 
Phantom peak Correlation 0.2045879 
Normalized Strand cross-correlation coefficient (NSC) 1.186365 
Relative Strand cross-correlation Coefficient (RSC) 1.313926 
Phantom Peak Quality Tag 1 
null device 
          1 

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

Num	13
ID	task.postalign_bed.pool_tag_pooled_rep.line_436.id_22
Name	pool_tag pooled_rep
Thread	thread_Root
PID	46449

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

Start	2017-04-07 19:02:15
End	2017-04-07 19:05:22
Elapsed	00:03:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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--------------------
16114 (process ID) old priority 0, new priority 19

Num	14
ID	task.postalign_bed.pool_tag_ppr1.line_436.id_23
Name	pool_tag ppr1
Thread	thread_Root
PID	46450

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

Start	2017-04-07 19:02:15
End	2017-04-07 19:03:49
Elapsed	00:01:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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--------------------
3261 (process ID) old priority 0, new priority 19

Num	15
ID	task.postalign_bed.pool_tag_ppr2.line_436.id_24
Name	pool_tag ppr2
Thread	thread_Root
PID	46451

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

Start	2017-04-07 19:02:17
End	2017-04-07 19:03:49
Elapsed	00:01:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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--------------------
3260 (process ID) old priority 0, new priority 19

Num	16
ID	task.callpeak_spp.spp_pooled_rep.line_59.id_25
Name	spp pooled_rep
Thread	thread_Root
PID	46452

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

Start	2017-04-07 19:05:24
End	2017-04-08 16:06:13
Elapsed	21:00:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz -p=2 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep -speak=255 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
9670 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 255 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 2 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz 
opened /tmp/46452.1.q/RtmpQM3kPR/ENCFF057NJA_ENCFF078YAS.tagAlign260039824ac0
done. read 115595584 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46452.1.q/RtmpQM3kPR/ss_50M_2000_GRCh38.nodup.tagAlign26006644261d
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.5698834 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.659704743088474 
Top 3 estimates for fragment length 255 
Window half size 630 
Phantom peak location 105 
Phantom peak Correlation 0.6325437 
Normalized Strand cross-correlation coefficient (NSC) 1.157614 
Relative Strand cross-correlation Coefficient (RSC) 1.433464 
Phantom Peak Quality Tag 1 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 1.018064  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.9822564  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000008 
Detected 1752810 peaks 

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

Num	17
ID	task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_26
Name	macs2 n/s pooled_rep
Thread	thread_Root
PID	46453

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-07 19:05:25
End	2017-04-07 19:05:25
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep -o "ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep -o "ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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--------------------
4555 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46453
exec_file:                  job_scripts/46453
submission_time:            Fri Apr  7 19:05:25 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_26.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_26.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

Num	18
ID	task.callpeak_spp.spp_ppr1.line_59.id_27
Name	spp ppr1
Thread	thread_Root
PID	46454

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

Start	2017-04-07 19:05:26
End	2017-04-09 08:14:32
Elapsed	1 day 13:09:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1 -speak=255 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
4787 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 255 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign.gz 
opened /tmp/46454.1.q/RtmpQh9hjW/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign140b944b99f
done. read 57797794 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46454.1.q/RtmpQh9hjW/ss_50M_2000_GRCh38.nodup.tagAlign140b15e2869a
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.4271679 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.508695266388583 
Top 3 estimates for fragment length 255 
Window half size 600 
Phantom peak location 105 
Phantom peak Correlation 0.4808243 
Normalized Strand cross-correlation coefficient (NSC) 1.190856 
Relative Strand cross-correlation Coefficient (RSC) 1.519435 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 2.016212  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.4959795  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000002 
Detected 1472130 peaks 

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

Num	19
ID	task.callpeak_spp.spp_ppr2.line_59.id_28
Name	spp ppr2
Thread	thread_Root
PID	46455

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

Start	2017-04-07 19:05:28
End	2017-04-09 10:15:54
Elapsed	1 day 15:10:26
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2 -speak=255 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
4554 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 255 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign.gz 
opened /tmp/46455.1.q/Rtmptul14g/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign126923d452d1
done. read 57797790 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46455.1.q/Rtmptul14g/ss_50M_2000_GRCh38.nodup.tagAlign12699be079d
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.4271575 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.508880272259647 
Top 3 estimates for fragment length 255 
Window half size 600 
Phantom peak location 105 
Phantom peak Correlation 0.4808522 
Normalized Strand cross-correlation coefficient (NSC) 1.191318 
Relative Strand cross-correlation Coefficient (RSC) 1.52199 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 2.016132  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.4959993  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000014 
Detected 1472657 peaks 

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

Num	20
ID	task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_29
Name	macs2 n/s ppr1
Thread	thread_Root
PID	46456

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-07 19:05:49
End	2017-04-07 19:05:49
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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--------------------
4769 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46456
exec_file:                  job_scripts/46456
submission_time:            Fri Apr  7 19:05:49 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_29.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_29.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

Num	21
ID	task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_30
Name	macs2 n/s ppr2
Thread	thread_Root
PID	46457

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-07 19:06:04
End	2017-04-07 19:06:04
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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--------------------
5913 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46457
submission_time:            Fri Apr  7 19:06:04 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_30.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_30.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available

Num	22
ID	task.callpeak_spp.spp_rep1.line_59.id_31
Name	spp rep1
Thread	thread_Root
PID	46458

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

Start	2017-04-07 19:06:18
End	2017-04-09 09:13:36
Elapsed	1 day 14:07:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1 -speak=265 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
6529 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 265 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz 
opened /tmp/46458.1.q/Rtmpqp5gqH/ENCFF057NJA.tagAlign1b0318d41372
done. read 47187626 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46458.1.q/Rtmpqp5gqH/ss_50M_2000_GRCh38.nodup.tagAlign1b03627b4bec
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.3858532 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.463036138559998 
Top 3 estimates for fragment length 265 
Window half size 630 
Phantom peak location 105 
Phantom peak Correlation 0.4344991 
Normalized Strand cross-correlation coefficient (NSC) 1.200032 
Relative Strand cross-correlation Coefficient (RSC) 1.586629 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 2.479712  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.4032726  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000002 
Detected 1345579 peaks 

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

Num	23
ID	task.callpeak_macs2.macs2_n_s_rep1.line_66.id_32
Name	macs2 n/s rep1
Thread	thread_Root
PID	46475

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-08 16:06:16
End	2017-04-08 16:06:16
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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--------------------
16354 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46475
exec_file:                  job_scripts/46475
submission_time:            Sat Apr  8 16:06:16 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_32.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_32.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

Num	24
ID	task.callpeak_spp.spp_rep1_pr1.line_59.id_33
Name	spp rep1-pr1
Thread	thread_Root
PID	46476

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

Start	2017-04-08 16:06:17
End	2017-04-10 04:18:26
Elapsed	1 day 12:12:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1 -speak=265 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
16345 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 265 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz 
opened /tmp/46476.1.q/RtmpQzZQo0/ENCFF057NJA.pr1.tagAlign40656aee589
done. read 23593814 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46476.1.q/RtmpQzZQo0/ss_50M_2000_GRCh38.nodup.tagAlign40651bb51799
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.2535152 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.314260048546272 
Top 3 estimates for fragment length 265 
Window half size 590 
Phantom peak location 105 
Phantom peak Correlation 0.2879675 
Normalized Strand cross-correlation coefficient (NSC) 1.23961 
Relative Strand cross-correlation Coefficient (RSC) 1.763157 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 4.892913  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2043772  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000006 
Detected 982887 peaks 

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

Num	25
ID	task.callpeak_spp.spp_rep1_pr2.line_59.id_34
Name	spp rep1-pr2
Thread	thread_Root
PID	46477

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

Start	2017-04-08 16:06:34
End	2017-04-10 04:27:52
Elapsed	1 day 12:21:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2 -speak=265 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
16527 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 265 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.gz 
opened /tmp/46477.1.q/RtmpXklNpc/ENCFF057NJA.pr2.tagAlign40e96a32787c
done. read 23593812 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46477.1.q/RtmpXklNpc/ss_50M_2000_GRCh38.nodup.tagAlign40e917e76833
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.2534986 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.314212112471067 
Top 3 estimates for fragment length 265 
Window half size 590 
Phantom peak location 105 
Phantom peak Correlation 0.2879123 
Normalized Strand cross-correlation coefficient (NSC) 1.239502 
Relative Strand cross-correlation Coefficient (RSC) 1.764227 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 4.891037  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2044556  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2 
Detected 983563 peaks 

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

Num	26
ID	task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_35
Name	macs2 n/s rep1-pr1
Thread	thread_Root
PID	46486

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-09 08:14:35
End	2017-04-09 08:14:35
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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--------------------
5551 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46486
exec_file:                  job_scripts/46486
submission_time:            Sun Apr  9 08:14:35 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_35.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_35.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

Num	27
ID	task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_36
Name	macs2 n/s rep1-pr2
Thread	thread_Root
PID	46487

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-09 08:14:48
End	2017-04-09 08:14:48
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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--------------------
5663 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46487
submission_time:            Sun Apr  9 08:14:48 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_36.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_36.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available

Num	28
ID	task.callpeak_spp.spp_rep2.line_59.id_37
Name	spp rep2
Thread	thread_Root
PID	46488

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

Start	2017-04-09 08:15:03
End	2017-04-10 22:08:17
Elapsed	1 day 13:53:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2 -speak=245 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
5780 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 245 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz 
opened /tmp/46488.1.q/RtmpSUtEMl/ENCFF078YAS.tagAlign16ea5f828553
done. read 68407958 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46488.1.q/RtmpSUtEMl/ss_50M_2000_GRCh38.nodup.tagAlign16ea30f314ac
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.4619778 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.547642597890246 
Top 3 estimates for fragment length 245 
Window half size 575 
Phantom peak location 105 
Phantom peak Correlation 0.5192385 
Normalized Strand cross-correlation coefficient (NSC) 1.185431 
Relative Strand cross-correlation Coefficient (RSC) 1.496048 
Phantom Peak Quality Tag 1 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 1.699441  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.5884286  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000002 
Detected 1588562 peaks 

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

Num	29
ID	task.callpeak_macs2.macs2_n_s_rep2.line_66.id_38
Name	macs2 n/s rep2
Thread	thread_Root
PID	46490

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-09 09:13:39
End	2017-04-09 09:13:39
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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--------------------
3647 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46490
exec_file:                  job_scripts/46490
submission_time:            Sun Apr  9 09:13:39 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_38.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_38.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

Num	30
ID	task.callpeak_spp.spp_rep2_pr1.line_59.id_39
Name	spp rep2-pr1
Thread	thread_Root
PID	46491

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

Start	2017-04-09 09:14:03
End	2017-04-11 02:34:37
Elapsed	1 day 17:20:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1 -speak=245 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
3774 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 245 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz 
opened /tmp/46491.1.q/RtmpnTbiw4/ENCFF078YAS.pr1.tagAlignf1471eb71d8
done. read 34203980 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46491.1.q/RtmpnTbiw4/ss_50M_2000_GRCh38.nodup.tagAlignf14791632bc
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.3198148 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.392125336597649 
Top 3 estimates for fragment length 245 
Window half size 540 
Phantom peak location 105 
Phantom peak Correlation 0.3638285 
Normalized Strand cross-correlation coefficient (NSC) 1.226101 
Relative Strand cross-correlation Coefficient (RSC) 1.642911 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 3.36103  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2975278  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000007 
Detected 1205133 peaks 

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

Num	31
ID	task.callpeak_spp.spp_rep2_pr2.line_59.id_40
Name	spp rep2-pr2
Thread	thread_Root
PID	46492

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

Start	2017-04-09 10:15:57
End	2017-04-10 18:44:50
Elapsed	1 day 08:28:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 61

 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 64

 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 68

 Rscript  ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2 -speak=245 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 82

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 84

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/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/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 90

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

   
--------------------Stdout--------------------
5460 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 245 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.gz 
opened /tmp/46492.1.q/RtmpYWS1rx/ENCFF078YAS.pr2.tagAlign16ba27e98214
done. read 34203978 fragments
ChIP data read length 101 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz 
opened /tmp/46492.1.q/RtmpYWS1rx/ss_50M_2000_GRCh38.nodup.tagAlign16ba5780f432
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.3198968 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.392218793950559 
Top 3 estimates for fragment length 245 
Window half size 540 
Phantom peak location 105 
Phantom peak Correlation 0.3639143 
Normalized Strand cross-correlation coefficient (NSC) 1.226079 
Relative Strand cross-correlation Coefficient (RSC) 1.643031 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 3.361849  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2974553  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000006 
Detected 1203654 peaks 

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

Num	32
ID	task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_41
Name	macs2 n/s rep2-pr1
Thread	thread_Root
PID	46502

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-10 04:18:29
End	2017-04-10 04:18:29
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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--------------------
33759 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46502
exec_file:                  job_scripts/46502
submission_time:            Mon Apr 10 04:18:29 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_41.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_41.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

Num	33
ID	task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_42
Name	macs2 n/s rep2-pr2
Thread	thread_Root
PID	46503

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus
Mem

Start	2017-04-10 04:18:49
End	2017-04-10 04:18:49
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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--------------------
33874 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46503
exec_file:                  job_scripts/46503
submission_time:            Mon Apr 10 04:18:49 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_42.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/chipseq.bds.20170407_180225_971/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_42.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36584.ZBTB17_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, ZBTB17_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB17_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, $]
bool	canFail	false
string	CPATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
string	EVENT_NOEPOLL	1
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_CCx82k
string	LANG	en_US.UTF-8
string	LIBRARY_PATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts//exec:/users/imk1/edirect:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_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/ZBTB17_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	36584.ZBTB17_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