Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170407_180218_777
Start time	2017-04-07 18:02:18
Run time	2 days 20:31:42.817
Tasks executed	33
Tasks failed	9
Tasks failed names	macs2 n/s rep1 macs2 n/s rep2 macs2 n/s rep2-pr2 macs2 n/s ppr2 macs2 n/s rep1-pr2 macs2 n/s ppr1 macs2 n/s rep2-pr1 macs2 n/s pooled_rep macs2 n/s rep1-pr1
Arguments*	[-title, ZIC2_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZIC2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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_180218_777/task.postalign_bed.pool_tag_pooled_rep.line_436.id_22 chipseq.bds.20170407_180218_777/task.postalign_bed.pool_tag_ppr1.line_436.id_23 chipseq.bds.20170407_180218_777/task.postalign_bed.pool_tag_ppr2.line_436.id_24 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_pooled_rep.line_59.id_25 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_26 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_ppr1.line_59.id_27 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_ppr2.line_59.id_28 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_29 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_30 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_rep1.line_59.id_31 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_32 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_rep1_pr1.line_59.id_33 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_rep1_pr2.line_59.id_34 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_35 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_36 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_rep2.line_59.id_37 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_38 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_rep2_pr1.line_59.id_39 chipseq.bds.20170407_180218_777/task.callpeak_spp.spp_rep2_pr2.line_59.id_40 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_41 chipseq.bds.20170407_180218_777/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_42
thread_43	thread_Root
thread_42	thread_Root	chipseq.bds.20170407_180218_777_parallel_42/task.postalign_bam.nmsrt_bam_rep2.line_495.id_10 chipseq.bds.20170407_180218_777_parallel_42/task.postalign_bam.bam_to_bedpe_rep2.line_602.id_16 chipseq.bds.20170407_180218_777_parallel_42/task.postalign_bam.bedpe_to_tag_rep2.line_640.id_18 chipseq.bds.20170407_180218_777_parallel_42/task.postalign_bed.subsample_bedpe2tag_rep2.line_115.id_19 chipseq.bds.20170407_180218_777_parallel_42/task.postalign_bed.spr_PE_rep2.line_299.id_20 chipseq.bds.20170407_180218_777_parallel_42/task.postalign_bed.xcor_rep2.line_212.id_21
thread_41	thread_Root	chipseq.bds.20170407_180218_777_parallel_41/task.postalign_bam.nmsrt_bam_rep1.line_495.id_11 chipseq.bds.20170407_180218_777_parallel_41/task.postalign_bam.bam_to_bedpe_rep1.line_602.id_12 chipseq.bds.20170407_180218_777_parallel_41/task.postalign_bam.bedpe_to_tag_rep1.line_640.id_13 chipseq.bds.20170407_180218_777_parallel_41/task.postalign_bed.subsample_bedpe2tag_rep1.line_115.id_14 chipseq.bds.20170407_180218_777_parallel_41/task.postalign_bed.spr_PE_rep1.line_299.id_15 chipseq.bds.20170407_180218_777_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_17

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.postalign_bam.nmsrt_bam_rep2.line_495.id_10
Name	nmsrt_bam rep2
Thread	thread_42
PID	46375

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

Start	2017-04-07 18:02:22
End	2017-04-07 18:39:15
Elapsed	00:36:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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--------------------
13497 (process ID) old priority 0, new priority 19

Num	2
ID	task.postalign_bam.nmsrt_bam_rep1.line_495.id_11
Name	nmsrt_bam rep1
Thread	thread_41
PID	46376

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

Start	2017-04-07 18:02:22
End	2017-04-07 18:33:08
Elapsed	00:30:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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--------------------
35688 (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	46419

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

Start	2017-04-07 18:33:10
End	2017-04-07 18:36:34
Elapsed	00:03:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.nmsrt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.nmsrt.bam | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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--------------------
48943 (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	46421

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

Start	2017-04-07 18:36:36
End	2017-04-07 18:38:24
Elapsed	00:01:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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--------------------
50567 (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	46422

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

Start	2017-04-07 18:38:25
End	2017-04-07 18:39:46
Elapsed	00:01:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bedpe.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bedpe.gz | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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--------------------
51231 (process ID) old priority 0, new priority 19

Num	6
ID	task.postalign_bed.spr_PE_rep1.line_299.id_15
Name	spr_PE rep1
Thread	thread_41
PID	46423

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

Start	2017-04-07 18:38:26
End	2017-04-07 18:41:33
Elapsed	00:03:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bedpe.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bedpe.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.  

# 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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.00" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz

# SYS command. line 314

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.01" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz

# SYS command. line 317

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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--------------------
51230 (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	46425

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

Start	2017-04-07 18:39:16
End	2017-04-07 18:43:04
Elapsed	00:03:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.nmsrt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.nmsrt.bam | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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--------------------
43776 (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	46429

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

Start	2017-04-07 18:41:35
End	2017-04-07 18:51:56
Elapsed	00:10:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.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--------------------
9419 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_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/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep1/ENCFF558PHY.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.15M.tagAlign.gz 
opened /tmp/46429.1.q/RtmpRuOUIA/ENCFF558PHY.15M.tagAlign25051b07819b
done. read 15000000 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1717122 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.211507598849921 
Top 3 estimates for fragment length 215 
Window half size 465 
Phantom peak location 105 
Phantom peak Correlation 0.1978346 
Normalized Strand cross-correlation coefficient (NSC) 1.231756 
Relative Strand cross-correlation Coefficient (RSC) 1.523419 
Phantom Peak Quality Tag 2 
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	46431

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

Start	2017-04-07 18:43:05
End	2017-04-07 18:44:33
Elapsed	00:01:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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--------------------
53105 (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	46432

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

Start	2017-04-07 18:44:35
End	2017-04-07 18:45:45
Elapsed	00:01:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bedpe.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bedpe.gz | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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--------------------
47813 (process ID) old priority 0, new priority 19
Waiting for 12 seconds.

Num	11
ID	task.postalign_bed.spr_PE_rep2.line_299.id_20
Name	spr_PE rep2
Thread	thread_42
PID	46433

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

Start	2017-04-07 18:44:36
End	2017-04-07 18:47:32
Elapsed	00:02:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bedpe.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bedpe.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bedpe.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.  

# 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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.00" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz

# SYS command. line 314

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.01" | \
			gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz

# SYS command. line 317

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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--------------------
48066 (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	46435

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

Start	2017-04-07 18:47:33
End	2017-04-07 18:57:50
Elapsed	00:10:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.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--------------------
9522 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_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/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/qc/rep2/ENCFF645WYX.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.15M.tagAlign.gz 
opened /tmp/46435.1.q/RtmpYUV9Bi/ENCFF645WYX.15M.tagAlign256c724949b7
done. read 15000000 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.171108 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.222812708815838 
Top 3 estimates for fragment length 210 
Window half size 455 
Phantom peak location 105 
Phantom peak Correlation 0.2056397 
Normalized Strand cross-correlation coefficient (NSC) 1.302176 
Relative Strand cross-correlation Coefficient (RSC) 1.497311 
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	46439

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

Start	2017-04-07 18:57:52
End	2017-04-07 19:00:52
Elapsed	00:03:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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--------------------
11638 (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	46440

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

Start	2017-04-07 18:57:53
End	2017-04-07 18:59:37
Elapsed	00:01:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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--------------------
11640 (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	46441

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

Start	2017-04-07 18:57:54
End	2017-04-07 18:59:44
Elapsed	00:01:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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--------------------
11639 (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	46442

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

Start	2017-04-07 19:00:55
End	2017-04-08 12:07:31
Elapsed	17:06:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_rep -speak=213 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.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--------------------
2744 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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 213 
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/ZIC2_MACS2/out/peak/spp/pooled_rep 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz 
opened /tmp/46442.1.q/RtmpWchBL0/ENCFF558PHY_ENCFF645WYX.tagAlignb233f535720
done. read 108422852 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/46442.1.q/RtmpWchBL0/ss_50M_2000_GRCh38.nodup.tagAlignb23a01d095
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.5393414 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.643380929388023 
Top 3 estimates for fragment length 213 
Window half size 470 
Phantom peak location 105 
Phantom peak Correlation 0.606489 
Normalized Strand cross-correlation coefficient (NSC) 1.192901 
Relative Strand cross-correlation Coefficient (RSC) 1.549415 
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= 1.0529  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.9497582  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 6.683097 
Detected 1011329 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	46443

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

Start	2017-04-07 19:00:56
End	2017-04-07 19:00:56
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.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--------------------
14256 (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:                 46443
exec_file:                  job_scripts/46443
submission_time:            Fri Apr  7 19:00:56 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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	46444

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

Start	2017-04-07 19:00:57
End	2017-04-09 03:59:09
Elapsed	1 day 08:58:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1 -speak=213 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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--------------------
14258 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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 213 
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/ZIC2_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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.gz 
opened /tmp/46444.1.q/Rtmp9AaaQm/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign38c94ceca436
done. read 54211426 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/46444.1.q/Rtmp9AaaQm/ss_50M_2000_GRCh38.nodup.tagAlign38c947a48a2b
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.3952465 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.499407230931669 
Top 3 estimates for fragment length 213 
Window half size 445 
Phantom peak location 105 
Phantom peak Correlation 0.4579356 
Normalized Strand cross-correlation coefficient (NSC) 1.263533 
Relative Strand cross-correlation Coefficient (RSC) 1.661545 
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= 2.092386  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.4779232  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.465795 
Detected 1578934 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	46445

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

Start	2017-04-07 19:00:57
End	2017-04-09 06:02:47
Elapsed	1 day 11:01:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2 -speak=213 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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--------------------
14257 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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 213 
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/ZIC2_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/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.gz 
opened /tmp/46445.1.q/RtmpIpdHwp/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign38da5618113f
done. read 54211426 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/46445.1.q/RtmpIpdHwp/ss_50M_2000_GRCh38.nodup.tagAlign38da2d8b1ab1
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.3952157 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.499534797612537 
Top 3 estimates for fragment length 213 
Window half size 445 
Phantom peak location 105 
Phantom peak Correlation 0.4579356 
Normalized Strand cross-correlation coefficient (NSC) 1.263955 
Relative Strand cross-correlation Coefficient (RSC) 1.663254 
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= 2.092545  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.477887  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.460572 
Detected 1581893 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	46446

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

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

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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--------------------
15035 (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:                 46446
exec_file:                  job_scripts/46446
submission_time:            Fri Apr  7 19:01:18 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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	46447

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

Start	2017-04-07 19:01:34
End	2017-04-07 19:01:34
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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--------------------
15423 (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:                 46447
submission_time:            Fri Apr  7 19:01:34 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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	46448

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

Start	2017-04-07 19:01:48
End	2017-04-09 09:03:04
Elapsed	1 day 14:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/rep1 -speak=215 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.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--------------------
15673 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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 215 
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/ZIC2_MACS2/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz 
opened /tmp/46448.1.q/RtmpC3MgBL/ENCFF558PHY.tagAlign3de365a17927
done. read 54689796 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/46448.1.q/RtmpC3MgBL/ss_50M_2000_GRCh38.nodup.tagAlign3de32e62f36e
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.4006823 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.495368691673384 
Top 3 estimates for fragment length 215 
Window half size 445 
Phantom peak location 105 
Phantom peak Correlation 0.4559186 
Normalized Strand cross-correlation coefficient (NSC) 1.236313 
Relative Strand cross-correlation Coefficient (RSC) 1.714206 
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= 2.045993  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.4887602  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.583138 
Detected 1561424 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	46459

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

Start	2017-04-08 12:07:33
End	2017-04-08 12:07:33
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1 -o "ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1 -o "ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.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--------------------
52653 (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:                 46459
submission_time:            Sat Apr  8 12:07:33 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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	24
ID	task.callpeak_spp.spp_rep1_pr1.line_59.id_33
Name	spp rep1-pr1
Thread	thread_Root
PID	46460

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

Start	2017-04-08 12:07:34
End	2017-04-09 18:43:42
Elapsed	1 day 06:36:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1 -speak=215 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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--------------------
13469 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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 215 
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/ZIC2_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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz 
opened /tmp/46460.1.q/RtmpVKnkjN/ENCFF558PHY.pr1.tagAlign34f3de9b460
done. read 27344898 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/46460.1.q/RtmpVKnkjN/ss_50M_2000_GRCh38.nodup.tagAlign34f344878e4
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.2671508 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.346779602029806 
Top 3 estimates for fragment length 215 
Window half size 420 
Phantom peak location 105 
Phantom peak Correlation 0.3082116 
Normalized Strand cross-correlation coefficient (NSC) 1.298067 
Relative Strand cross-correlation Coefficient (RSC) 1.939291 
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= 4.057101  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2464814  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000016 
Detected 1216459 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	46461

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

Start	2017-04-08 12:07:49
End	2017-04-09 12:55:05
Elapsed	1 day 00:47:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2 -speak=215 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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--------------------
53272 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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 215 
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/ZIC2_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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz 
opened /tmp/46461.1.q/Rtmp2qKVoO/ENCFF558PHY.pr2.tagAlignd1791afcfa7f
done. read 27344898 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/46461.1.q/Rtmp2qKVoO/ss_50M_2000_GRCh38.nodup.tagAlignd1796af315ad
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.2671596 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.346627485243094 
Top 3 estimates for fragment length 215 
Window half size 420 
Phantom peak location 105 
Phantom peak Correlation 0.3082459 
Normalized Strand cross-correlation coefficient (NSC) 1.297455 
Relative Strand cross-correlation Coefficient (RSC) 1.934168 
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= 4.058601  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2463903  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000036 
Detected 1215850 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	46481

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

Start	2017-04-09 03:59:11
End	2017-04-09 03:59:11
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.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--------------------
8685 (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:                 46481
exec_file:                  job_scripts/46481
submission_time:            Sun Apr  9 03:59:11 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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	46482

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

Start	2017-04-09 03:59:33
End	2017-04-09 03:59:33
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.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--------------------
8799 (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:                 46482
exec_file:                  job_scripts/46482
submission_time:            Sun Apr  9 03:59:33 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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	28
ID	task.callpeak_spp.spp_rep2.line_59.id_37
Name	spp rep2
Thread	thread_Root
PID	46483

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

Start	2017-04-09 03:59:48
End	2017-04-10 09:43:51
Elapsed	1 day 05:44:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/rep2 -speak=210 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.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--------------------
8916 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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 210 
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/ZIC2_MACS2/out/peak/spp/rep2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz 
opened /tmp/46483.1.q/RtmpgaOxY0/ENCFF645WYX.tagAlign232d1f41cbc1
done. read 53733056 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/46483.1.q/RtmpgaOxY0/ss_50M_2000_GRCh38.nodup.tagAlign232d7678fa5d
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.3895359 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.504086793895638 
Top 3 estimates for fragment length 210 
Window half size 440 
Phantom peak location 105 
Phantom peak Correlation 0.4601011 
Normalized Strand cross-correlation coefficient (NSC) 1.29407 
Relative Strand cross-correlation Coefficient (RSC) 1.623334 
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= 2.141468  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.4669695  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.385967 
Detected 1583128 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	46484

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

Start	2017-04-09 06:02:49
End	2017-04-09 06:02:49
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2 -o "ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2 -o "ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.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--------------------
2491 (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:                 46484
exec_file:                  job_scripts/46484
submission_time:            Sun Apr  9 06:02:49 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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=00:00:01, mem=0.07426 GBs, io=0.07678, vmem=38.508M, maxvmem=229.203M
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	46485

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

Start	2017-04-09 06:03:02
End	2017-04-10 14:34:01
Elapsed	1 day 08:30:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1 -speak=210 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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--------------------
2617 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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 210 
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/ZIC2_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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz 
opened /tmp/46485.1.q/RtmpPyUpzJ/ENCFF645WYX.pr1.tagAligna9779a31cdb
done. read 26866528 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/46485.1.q/RtmpPyUpzJ/ss_50M_2000_GRCh38.nodup.tagAligna976f4d97a4
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.2605403 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.356517011803149 
Top 3 estimates for fragment length 210 
Window half size 420 
Phantom peak location 105 
Phantom peak Correlation 0.3138152 
Normalized Strand cross-correlation coefficient (NSC) 1.368376 
Relative Strand cross-correlation Coefficient (RSC) 1.801538 
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= 4.24332  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2356645  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000007 
Detected 1162182 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	46489

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

Start	2017-04-09 09:03:07
End	2017-04-10 09:34:27
Elapsed	1 day 00:31:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2 -speak=210 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.ccscore

# SYS command. line 72

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak.gz

# SYS command. line 76

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pdf

# SYS command. line 79

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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--------------------
21973 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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 210 
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/ZIC2_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/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_VS_ss_50M_2000_GRCh38.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/spp/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz 
opened /tmp/46489.1.q/Rtmp65FCDU/ENCFF645WYX.pr2.tagAlign572b344bc71d
done. read 26866528 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/46489.1.q/Rtmp65FCDU/ss_50M_2000_GRCh38.nodup.tagAlign572b185645d7
done. read 99493262 fragments
Control data read length 101 
Calculating peak characteristics
Minimum cross-correlation value 0.2606804 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.35665593868338 
Top 3 estimates for fragment length 210 
Window half size 415 
Phantom peak location 105 
Phantom peak Correlation 0.3138473 
Normalized Strand cross-correlation coefficient (NSC) 1.368173 
Relative Strand cross-correlation Coefficient (RSC) 1.805174 
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= 4.243817  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.235637  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000001 
Detected 1167981 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	46493

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

Start	2017-04-09 12:55:08
End	2017-04-09 12:55:08
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.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--------------------
12185 (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:                 46493
submission_time:            Sun Apr  9 12:55:08 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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	33
ID	task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_42
Name	macs2 n/s rep2-pr2
Thread	thread_Root
PID	46494

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

Start	2017-04-09 12:55:33
End	2017-04-09 12:55:33
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.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--------------------
12318 (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:                 46494
submission_time:            Sun Apr  9 12:55:33 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/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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/ZIC2_MACS2/chipseq.bds.20170407_180218_777/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=36189.ZIC2_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/ZIC2_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

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, ZIC2_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZIC2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_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/ZIC2_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	36189.ZIC2_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