BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161113_130757_102
Start time 2016-11-13 13:07:57
Run time 07:23:05.826
Tasks executed 7
Tasks failed 1
Tasks failed names 
xcor rep1
Arguments* [-title, SRR1370886_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370886_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $]
System* sge
Cpus* -1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None
thread_42 thread_Root 
 chipseq.bds.20161113_130757_102_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_10
thread_41 thread_Root 
 chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_11
chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_12
chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_13
chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_14
chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bed.spr_rep1.line_255.id_15
chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_16

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.postalign_bam.bam_to_tag_ctl1.line_505.id_10
Name bam_to_tag ctl1
Thread thread_42
PID 9021
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-13 13:07:59
End 2016-11-13 13:15:23
Elapsed 00:07:24
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Dependencies 
 
# SYS command. line 507

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

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
10261 (process ID) old priority 0, new priority 10
Num 2
ID task.postalign_bam.markdup_bam_picard_rep1.line_348.id_11
Name markdup_bam_picard rep1
Thread thread_41
PID 9022
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 1
Mem
Start 2016-11-13 13:07:59
End 2016-11-13 13:12:31
Elapsed 00:04:32
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.dup.qc
Dependencies 
 
# SYS command. line 350

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

# SYS command. line 354

 export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"

# SYS command. line 360

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 369

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 381

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
10260 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Nov 13 13:08:20 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Nov 13 13:08:20 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-13 13:08:20	MarkDuplicates	Start of doWork freeMemory: 254879488; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-13 13:08:20	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-13 13:08:20	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-13 13:08:25	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr1:93,083,166
INFO	2016-11-13 13:08:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:29	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    3s.  Last read position: chr1:228,173,842
INFO	2016-11-13 13:08:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:32	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    3s.  Last read position: chr2:144,263,129
INFO	2016-11-13 13:08:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:35	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    2s.  Last read position: chr3:61,247,241
INFO	2016-11-13 13:08:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:38	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    2s.  Last read position: chr4:66,490,141
INFO	2016-11-13 13:08:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:42	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    3s.  Last read position: chr5:68,415,891
INFO	2016-11-13 13:08:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:45	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    3s.  Last read position: chr6:10,415,000
INFO	2016-11-13 13:08:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:48	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    3s.  Last read position: chr6:147,253,177
INFO	2016-11-13 13:08:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:51	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    3s.  Last read position: chr7:137,470,339
INFO	2016-11-13 13:08:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:54	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    2s.  Last read position: chr9:5,415,036
INFO	2016-11-13 13:08:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:08:59	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    4s.  Last read position: chr10:37,297,980
INFO	2016-11-13 13:08:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:02	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    2s.  Last read position: chr11:31,770,284
INFO	2016-11-13 13:09:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:05	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    3s.  Last read position: chr12:49,197,507
INFO	2016-11-13 13:09:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:08	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr13:52,351,689
INFO	2016-11-13 13:09:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:12	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    3s.  Last read position: chr15:41,004,632
INFO	2016-11-13 13:09:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:14	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    2s.  Last read position: chr16:58,464,097
INFO	2016-11-13 13:09:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:17	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chr17:66,348,816
INFO	2016-11-13 13:09:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:22	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    4s.  Last read position: chr19:15,261,117
INFO	2016-11-13 13:09:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:25	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    3s.  Last read position: chr20:44,766,013
INFO	2016-11-13 13:09:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:29	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    3s.  Last read position: chrX:17,112,108
INFO	2016-11-13 13:09:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 13:09:31	MarkDuplicates	Read 20991724 records. 0 pairs never matched.
INFO	2016-11-13 13:09:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3239279824; totalMemory: 4993318912; maxMemory: 11453595648
INFO	2016-11-13 13:09:34	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-13 13:09:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-13 13:09:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-13 13:09:36	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-13 13:09:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 4940161960; totalMemory: 7861698560; maxMemory: 11453595648
INFO	2016-11-13 13:09:37	MarkDuplicates	Marking 2606962 records as duplicates.
INFO	2016-11-13 13:09:37	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-13 13:10:56	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:19s.  Time for last 10,000,000:   79s.  Last read position: chr9:5,415,036
INFO	2016-11-13 13:12:22	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:45s.  Time for last 10,000,000:   85s.  Last read position: chrX:17,112,108
INFO	2016-11-13 13:12:31	MarkDuplicates	Before output close freeMemory: 8408441880; totalMemory: 8482455552; maxMemory: 11453595648
INFO	2016-11-13 13:12:31	MarkDuplicates	After output close freeMemory: 8234377104; totalMemory: 8308391936; maxMemory: 11453595648
[Sun Nov 13 13:12:31 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.17 minutes.
Runtime.totalMemory()=8308391936
Num 3
ID task.postalign_bam.dedup_bam_2_rep1.line_144.id_12
Name dedup_bam_2 rep1
Thread thread_41
PID 9251
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-13 13:12:33
End 2016-11-13 15:02:38
Elapsed 01:50:04
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.pbc.qc
Dependencies 
 
# SYS command. line 146

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

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.pbc.qc

# SYS command. line 169

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
55905 (process ID) old priority 0, new priority 10
Num 4
ID task.postalign_bam.bam_to_tag_rep1.line_505.id_13
Name bam_to_tag rep1
Thread thread_41
PID 9408
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-13 15:02:40
End 2016-11-13 16:46:03
Elapsed 01:43:23
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz
Dependencies 
 
# SYS command. line 507

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

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
5351 (process ID) old priority 0, new priority 10
Num 5
ID task.postalign_bed.subsample_tag_rep1.line_45.id_14
Name subsample_tag rep1
Thread thread_41
PID 9597
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-13 16:46:05
End 2016-11-13 19:12:55
Elapsed 02:26:50
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.15M.tagAlign.gz
Dependencies 
 
# SYS command. line 47

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

# SYS command. line 50

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.15M.tagAlign.gz

# SYS command. line 53

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
54244 (process ID) old priority 0, new priority 10
Waiting for 29 seconds.
Num 6
ID task.postalign_bed.spr_rep1.line_255.id_15
Name spr rep1
Thread thread_41
PID 9598
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-13 16:46:05
End 2016-11-13 19:13:38
Elapsed 02:27:32
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.gz
Dependencies 
 
# SYS command. line 257

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

# SYS command. line 260

 nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz | wc -l )

# SYS command. line 261

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

# SYS command. line 265

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.01

# SYS command. line 273

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
24835 (process ID) old priority 0, new priority 10
Num 7
ID task.postalign_bed.xcor_rep1.line_212.id_16
Name xcor rep1
Thread thread_41
PID 9749
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2016-11-13 19:13:39
End 2016-11-13 19:13:39
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.15M.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.plot.pdf
Dependencies 
 
# SYS command. line 214

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

# SYS command. line 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/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.15M.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.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--------------------
48561 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.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: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/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/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.nodup.15M.tagAlign.gz 
opened /tmp/9749.1.q/RtmpmoO5Vw/SRR1370886_1.nodup.15M.tagAlignbe026139f0c8
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1735547 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.266724316314493 
Top 3 estimates for fragment length 145 
Window half size 300 
Phantom peak location 55 
Phantom peak Correlation 0.2289182 
Normalized Strand cross-correlation coefficient (NSC) 1.536832 
Relative Strand cross-correlation Coefficient (RSC) 1.682869 
Phantom Peak Quality Tag 2 

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3 
Error in pdf(file = iparams$output.plot.file, width = 5, height = 5) : 
  failed to load default encoding
In addition: Warning message:
In pdf(file = iparams$output.plot.file, width = 5, height = 5) :
  failed to load encoding file 'ISOLatin1.enc'
Execution halted

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 9749
exec_file:                  job_scripts/9749
submission_time:            Sun Nov 13 19:13:39 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_16.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/chipseq.bds.20161113_130757_102_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_16.stdout.cluster
jobshare:                   0
env_list:                   MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,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_private/deeplift,SSH_TTY=/dev/pts/4,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,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=/software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect,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=8592.SRR1370886_1.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,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/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/HughesZnfData/SRR1370886_1,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6,SSH_CONNECTION=171.65.77.8 55144 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/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:19:29, mem=339.43764 GBs, io=1.59052, vmem=968.559M, maxvmem=1.037G
scheduling info:            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@kali" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            queue instance "q@surya" dropped because it is full
                            queue instance "q@kadru" dropped because it is full

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
string _LMFILES_ /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6
bool allowEmpty false
string[] args [-title, SRR1370886_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370886_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $]
string ASCPKEY /software/ascp/etc/asperaweb_id_dsa.openssh
bool canFail false
int cpus -1
int cpusLocal 56
int day 86400
string DEEPLIFT_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:12.0
real E 2.718281828459045
string ENHANCER_SCRIPTS_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KERAS_DIR /users/imk1/.local/lib/python2.7/site-packages/keras/
string KRB5CCNAME FILE:/tmp/krb5cc_1048_N5SeQf
string LANG en_US.UTF-8
string LOADEDMODULES modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string MODULESAPPSDIR /software
string MODULESHOME /software/env_module/3.2.10
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string node
int P 1125899906842624
string PATH /software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
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/HughesZnfData/SRR1370886_1
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/HughesZnfData/SRR1370886_1
string PYTHONPATH /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string queue
int retry 0
string RULEFITBASE /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string SHELL /bin/bash
string SHLVL 3
string SSH_CLIENT 171.65.77.8 55144 22
string SSH_CONNECTION 171.65.77.8 55144 171.65.76.63 22
string SSH_TTY /dev/pts/4
string STY 8592.SRR1370886_1.BDS
string system sge
int T 1099511627776
string TERM screen
string TERMCAP SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int timeout -1
string USER imk1
string UTIL_SCRIPTS_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int walltimeout 8640000
int week 604800
string WINDOW 0
string XDG_RUNTIME_DIR /run/user/1048
string XDG_SESSION_ID 20
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt