BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161110_170951_228
Start time 2016-11-10 17:09:51
Run time 05:01:57.151
Tasks executed 8
Tasks failed 1
Tasks failed names 
markdup_bam_picard ctl1
Arguments* [-title, SRR1370879_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370879_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.20161110_170951_228_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10
chipseq.bds.20161110_170951_228_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_13
thread_41 thread_Root 
 chipseq.bds.20161110_170951_228_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_11
chipseq.bds.20161110_170951_228_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_12
chipseq.bds.20161110_170951_228_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_14
chipseq.bds.20161110_170951_228_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_15
chipseq.bds.20161110_170951_228_parallel_41/task.postalign_bed.spr_rep1.line_255.id_16
chipseq.bds.20161110_170951_228_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.dedup_bam_1_ctl1.line_95.id_10
Name dedup_bam_1 ctl1
Thread thread_42
PID 6884
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 4
Mem
Start 2016-11-10 17:09:52
End 2016-11-10 17:29:29
Elapsed 00:19:36
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Dependencies 
 
# SYS command. line 97

 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 105

 if [[ 0 > 0 ]]; then \
				sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
			    fi

# SYS command. line 116

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
32233 (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 6885
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 1
Mem
Start 2016-11-10 17:09:53
End 2016-11-10 17:11:36
Elapsed 00:01:42
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_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/SRR1370879_1/out/align/rep1/SRR1370879_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_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--------------------
29436 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 17:10:09 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_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
[Thu Nov 10 17:10:09 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	2016-11-10 17:10:10	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 17:10:10	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 17:10:10	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 17:10:16	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr2:148,830,525
INFO	2016-11-10 17:10:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:20	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    4s.  Last read position: chr5:14,491,473
INFO	2016-11-10 17:10:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:23	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    3s.  Last read position: chr7:46,159,247
INFO	2016-11-10 17:10:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:26	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    2s.  Last read position: chr10:92,805,939
INFO	2016-11-10 17:10:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:30	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    4s.  Last read position: chr14:64,067,952
INFO	2016-11-10 17:10:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:33	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    2s.  Last read position: chr19:29,294,208
INFO	2016-11-10 17:10:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:36	MarkDuplicates	Read 6941801 records. 0 pairs never matched.
INFO	2016-11-10 17:10:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2011039848; totalMemory: 2846359552; maxMemory: 11453595648
INFO	2016-11-10 17:10:37	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 17:10:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 17:10:38	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 17:10:39	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 17:10:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2809108168; totalMemory: 5711069184; maxMemory: 11453595648
INFO	2016-11-10 17:10:39	MarkDuplicates	Marking 1549282 records as duplicates.
INFO	2016-11-10 17:10:39	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-10 17:11:35	MarkDuplicates	Before output close freeMemory: 6071487200; totalMemory: 6118965248; maxMemory: 11453595648
INFO	2016-11-10 17:11:35	MarkDuplicates	After output close freeMemory: 6017484376; totalMemory: 6064963584; maxMemory: 11453595648
[Thu Nov 10 17:11:35 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.42 minutes.
Runtime.totalMemory()=6064963584
Num 3
ID task.postalign_bam.dedup_bam_2_rep1.line_144.id_12
Name dedup_bam_2 rep1
Thread thread_41
PID 6978
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 17:11:37
End 2016-11-10 18:32:16
Elapsed 01:20:39
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.dupmark.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_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/SRR1370879_1/out/align/rep1/SRR1370879_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_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/SRR1370879_1/out/qc/rep1/SRR1370879_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--------------------
15123 (process ID) old priority 0, new priority 10
Num 4
ID task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_13
Name markdup_bam_picard ctl1
Thread thread_42
PID 7154
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 1
Mem
Start 2016-11-10 17:29:30
End 2016-11-10 17:29:30
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/ctl1/ss_50M_2000_GRCh38.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/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/ctl1/ss_50M_2000_GRCh38.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--------------------
18877 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 19:48:58 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/ctl1/ss_50M_2000_GRCh38.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
[Thu Nov 10 19:48:58 PST 2016] Executing as imk1@wotan 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	2016-11-10 19:48:59	MarkDuplicates	Start of doWork freeMemory: 254877880; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 19:48:59	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 19:48:59	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 19:49:19	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:   18s.  Last read position: chr1:22,298,551
INFO	2016-11-10 19:49:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:35	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:   15s.  Last read position: chr1:41,895,424
INFO	2016-11-10 19:49:35	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:49:48	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:   13s.  Last read position: chr1:63,396,527
INFO	2016-11-10 19:49:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:50:06	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:   17s.  Last read position: chr1:89,147,707
INFO	2016-11-10 19:50:06	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:20	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:   14s.  Last read position: chr1:115,615,553
INFO	2016-11-10 19:50:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:33	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:   13s.  Last read position: chr1:164,468,682
INFO	2016-11-10 19:50:33	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:50:51	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:   17s.  Last read position: chr1:189,102,252
INFO	2016-11-10 19:50:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:51:03	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:   11s.  Last read position: chr1:213,979,760
INFO	2016-11-10 19:51:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:15	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:   12s.  Last read position: chr1:231,814,268
INFO	2016-11-10 19:51:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:28	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:   12s.  Last read position: chr2:3,652,468
INFO	2016-11-10 19:51:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:51:49	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:   20s.  Last read position: chr2:39,505,122
INFO	2016-11-10 19:51:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:02	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:   12s.  Last read position: chr2:73,561,393
INFO	2016-11-10 19:52:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:52:15	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:   13s.  Last read position: chr2:120,526,571
INFO	2016-11-10 19:52:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:29	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:   13s.  Last read position: chr2:160,316,783
INFO	2016-11-10 19:52:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:52	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:   22s.  Last read position: chr2:195,549,735
INFO	2016-11-10 19:52:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:06	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:   13s.  Last read position: chr2:230,358,034
INFO	2016-11-10 19:53:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:17	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:   10s.  Last read position: chr3:16,305,780
INFO	2016-11-10 19:53:17	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:53:30	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:   13s.  Last read position: chr3:49,251,279
INFO	2016-11-10 19:53:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:42	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:   11s.  Last read position: chr3:84,621,225
INFO	2016-11-10 19:53:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:04	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:   21s.  Last read position: chr3:128,121,129
INFO	2016-11-10 19:54:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:15	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:   11s.  Last read position: chr3:165,373,238
INFO	2016-11-10 19:54:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:28	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:   12s.  Last read position: chr3:195,333,247
INFO	2016-11-10 19:54:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:42	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:   13s.  Last read position: chr4:37,752,582
INFO	2016-11-10 19:54:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:55	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:   12s.  Last read position: chr4:81,286,306
INFO	2016-11-10 19:54:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:07	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:   11s.  Last read position: chr4:119,339,736
INFO	2016-11-10 19:55:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:31	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:   24s.  Last read position: chr4:158,818,783
INFO	2016-11-10 19:55:31	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:55:43	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:   11s.  Last read position: chr5:6,447,551
INFO	2016-11-10 19:55:43	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 19:55:55	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:06:54s.  Time for last 1,000,000:   11s.  Last read position: chr5:33,219,021
INFO	2016-11-10 19:55:55	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:56:06	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:   10s.  Last read position: chr5:60,694,078
INFO	2016-11-10 19:56:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:56:20	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:   13s.  Last read position: chr5:86,336,676
INFO	2016-11-10 19:56:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:33	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:   13s.  Last read position: chr5:112,930,184
INFO	2016-11-10 19:56:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:57:04	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:08:04s.  Time for last 1,000,000:   31s.  Last read position: chr5:136,852,889
INFO	2016-11-10 19:57:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:17	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:   12s.  Last read position: chr5:160,271,193
INFO	2016-11-10 19:57:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:30	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:08:29s.  Time for last 1,000,000:   12s.  Last read position: chr6:4,126,386
INFO	2016-11-10 19:57:30	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:57:42	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:08:41s.  Time for last 1,000,000:   12s.  Last read position: chr6:28,666,579
INFO	2016-11-10 19:57:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:55	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:   13s.  Last read position: chr6:49,527,281
INFO	2016-11-10 19:57:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:06	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:   10s.  Last read position: chr6:81,728,195
INFO	2016-11-10 19:58:06	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:18	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:   12s.  Last read position: chr6:107,535,760
INFO	2016-11-10 19:58:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:34	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:   15s.  Last read position: chr6:132,364,408
INFO	2016-11-10 19:58:34	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:47	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:09:47s.  Time for last 1,000,000:   13s.  Last read position: chr6:156,918,595
INFO	2016-11-10 19:58:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:00	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:   12s.  Last read position: chr7:18,636,743
INFO	2016-11-10 19:59:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:12	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:   12s.  Last read position: chr7:53,850,313
INFO	2016-11-10 19:59:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:22	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    9s.  Last read position: chr7:96,503,433
INFO	2016-11-10 19:59:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:30	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:10:29s.  Time for last 1,000,000:    8s.  Last read position: chr7:120,651,846
INFO	2016-11-10 19:59:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:15	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:  105s.  Last read position: chr7:146,401,497
INFO	2016-11-10 20:01:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:27	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:12:27s.  Time for last 1,000,000:   11s.  Last read position: chr8:17,030,519
INFO	2016-11-10 20:01:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:54	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:   26s.  Last read position: chr8:42,750,671
INFO	2016-11-10 20:01:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:02:24	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:13:23s.  Time for last 1,000,000:   30s.  Last read position: chr8:85,385,487
INFO	2016-11-10 20:02:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:02:46	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:13:45s.  Time for last 1,000,000:   22s.  Last read position: chr8:124,358,985
INFO	2016-11-10 20:02:46	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:03:17	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:14:16s.  Time for last 1,000,000:   30s.  Last read position: chr9:18,183,883
INFO	2016-11-10 20:03:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:03:46	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:14:46s.  Time for last 1,000,000:   29s.  Last read position: chr9:84,163,983
INFO	2016-11-10 20:03:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:04:18	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:15:17s.  Time for last 1,000,000:   31s.  Last read position: chr9:119,875,535
INFO	2016-11-10 20:04:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:04:52	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:15:51s.  Time for last 1,000,000:   33s.  Last read position: chr10:5,661,683
INFO	2016-11-10 20:04:52	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:06:01	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:17:00s.  Time for last 1,000,000:   69s.  Last read position: chr10:29,748,948
INFO	2016-11-10 20:06:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:06:41	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:17:40s.  Time for last 1,000,000:   40s.  Last read position: chr10:61,280,221
INFO	2016-11-10 20:06:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:07:26	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:18:25s.  Time for last 1,000,000:   44s.  Last read position: chr10:85,305,552
INFO	2016-11-10 20:07:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:08:16	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:19:15s.  Time for last 1,000,000:   50s.  Last read position: chr10:108,129,202
INFO	2016-11-10 20:08:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:09:07	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:20:06s.  Time for last 1,000,000:   50s.  Last read position: chr10:132,730,123
INFO	2016-11-10 20:09:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:10:15	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:21:14s.  Time for last 1,000,000:   67s.  Last read position: chr11:35,359,267
INFO	2016-11-10 20:10:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:10:55	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:21:55s.  Time for last 1,000,000:   40s.  Last read position: chr11:75,696,431
INFO	2016-11-10 20:10:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:11:37	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:22:37s.  Time for last 1,000,000:   41s.  Last read position: chr11:114,414,621
INFO	2016-11-10 20:11:37	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:12:19	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:23:18s.  Time for last 1,000,000:   41s.  Last read position: chr12:8,900,276
INFO	2016-11-10 20:12:19	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:13:45	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:24:45s.  Time for last 1,000,000:   86s.  Last read position: chr12:38,863,889
INFO	2016-11-10 20:13:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:14:25	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:25:24s.  Time for last 1,000,000:   39s.  Last read position: chr12:60,598,824
INFO	2016-11-10 20:14:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:15:00	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:26:00s.  Time for last 1,000,000:   35s.  Last read position: chr12:88,520,538
INFO	2016-11-10 20:15:00	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:15:36	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:26:36s.  Time for last 1,000,000:   35s.  Last read position: chr12:112,268,437
INFO	2016-11-10 20:15:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:15:59	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:26:58s.  Time for last 1,000,000:   22s.  Last read position: chr13:23,999,632
INFO	2016-11-10 20:15:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:16:38	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:27:37s.  Time for last 1,000,000:   39s.  Last read position: chr13:51,165,870
INFO	2016-11-10 20:16:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:17:13	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:28:12s.  Time for last 1,000,000:   35s.  Last read position: chr13:88,986,369
INFO	2016-11-10 20:17:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:18:05	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:29:05s.  Time for last 1,000,000:   52s.  Last read position: chr14:23,149,367
INFO	2016-11-10 20:18:05	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:18:41	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:29:40s.  Time for last 1,000,000:   35s.  Last read position: chr14:58,140,905
INFO	2016-11-10 20:18:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:19:20	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:30:19s.  Time for last 1,000,000:   38s.  Last read position: chr14:91,912,553
INFO	2016-11-10 20:19:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:20:45	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:31:44s.  Time for last 1,000,000:   85s.  Last read position: chr15:38,895,095
INFO	2016-11-10 20:20:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:22:18	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:33:18s.  Time for last 1,000,000:   93s.  Last read position: chr15:68,188,367
INFO	2016-11-10 20:22:18	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:23:21	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:34:20s.  Time for last 1,000,000:   62s.  Last read position: chr15:87,921,272
INFO	2016-11-10 20:23:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:25:02	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:36:01s.  Time for last 1,000,000:  101s.  Last read position: chr16:11,143,813
INFO	2016-11-10 20:25:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:26:19	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:37:18s.  Time for last 1,000,000:   77s.  Last read position: chr16:51,391,437
INFO	2016-11-10 20:26:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:27:25	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:38:24s.  Time for last 1,000,000:   65s.  Last read position: chr16:84,928,458
INFO	2016-11-10 20:27:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:29:17	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:40:17s.  Time for last 1,000,000:  112s.  Last read position: chr17:18,368,935
INFO	2016-11-10 20:29:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:32:44	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:43:43s.  Time for last 1,000,000:  206s.  Last read position: chr17:44,246,522
INFO	2016-11-10 20:32:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:37:15	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:48:15s.  Time for last 1,000,000:  271s.  Last read position: chr17:66,172,158
INFO	2016-11-10 20:37:15	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 20:38:34	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:49:33s.  Time for last 1,000,000:   78s.  Last read position: chr18:5,619,614
INFO	2016-11-10 20:38:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:41:33	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:52:32s.  Time for last 1,000,000:  179s.  Last read position: chr18:46,152,631
INFO	2016-11-10 20:41:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:43:15	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:54:14s.  Time for last 1,000,000:  101s.  Last read position: chr19:1,328,731
INFO	2016-11-10 20:43:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:46:57	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:57:56s.  Time for last 1,000,000:  222s.  Last read position: chr19:28,148,444
INFO	2016-11-10 20:46:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:57:47	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 01:08:47s.  Time for last 1,000,000:  650s.  Last read position: chr19:40,341,579
INFO	2016-11-10 20:57:47	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:58:59	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 01:09:58s.  Time for last 1,000,000:   71s.  Last read position: chr20:3,222,035
INFO	2016-11-10 20:58:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 21:02:03	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 01:13:02s.  Time for last 1,000,000:  184s.  Last read position: chr20:37,218,903
INFO	2016-11-10 21:02:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
/users/imk1/anaconda2/envs/aquas_chipseq/bin/picard: line 60: 18958 Killed                  java -Xms512m -Xmx1g -jar /users/imk1/anaconda2/envs/aquas_chipseq/share/picard-1.126-4/picard.jar MarkDuplicates INPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=false

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 7154
exec_file:                  job_scripts/7154
submission_time:            Thu Nov 10 17:29:30 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/SRR1370879_1
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/chipseq.bds.20161110_170951_228_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_13.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/chipseq.bds.20161110_170951_228_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_13.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=29021.SRR1370879_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/SRR1370879_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
parallel environment:  shm range: 1
usage    1:                 cpu=00:23:48, mem=4847.74575 GBs, io=50.32839, vmem=27.133M, maxvmem=3.514G
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
                            All queues dropped because of overload or full
Num 5
ID task.postalign_bam.bam_to_tag_rep1.line_505.id_14
Name bam_to_tag rep1
Thread thread_41
PID 7209
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 18:32:18
End 2016-11-10 20:19:18
Elapsed 01:46:59
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_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/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_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--------------------
22538 (process ID) old priority 0, new priority 10
Num 6
ID task.postalign_bed.subsample_tag_rep1.line_45.id_15
Name subsample_tag rep1
Thread thread_41
PID 7354
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 20:19:20
End 2016-11-10 21:27:01
Elapsed 01:07:40
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_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/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_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--------------------
17694 (process ID) old priority 0, new priority 10
Waiting for 45 seconds.
Num 7
ID task.postalign_bed.spr_rep1.line_255.id_16
Name spr rep1
Thread thread_41
PID 7355
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 20:19:21
End 2016-11-10 21:55:59
Elapsed 01:36:37
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr2/SRR1370879_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/SRR1370879_1/out/align/rep1/SRR1370879_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/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/pseudo_reps/rep1/pr1/SRR1370879_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--------------------
26115 (process ID) old priority 0, new priority 10
Num 8
ID task.postalign_bed.xcor_rep1.line_212.id_17
Name xcor rep1
Thread thread_41
PID 7568
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 21:56:01
End 2016-11-10 22:11:48
Elapsed 00:15:47
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.15M.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_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/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.15M.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_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--------------------
36076 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_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/SRR1370879_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/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/qc/rep1/SRR1370879_1.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out/align/rep1/SRR1370879_1.nodup.15M.tagAlign.gz 
opened /tmp/7568.1.q/RtmphWcHy8/SRR1370879_1.nodup.15M.tagAlign8db14731a6b8
done. read 5390449 fragments
ChIP data read length 51 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.07060774 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.0757908232486616,0.0756506521567927,0.0737251657171491 
Top 3 estimates for fragment length 65,85,160 
Window half size 220 
Phantom peak location 50 
Phantom peak Correlation 0.07602022 
Normalized Strand cross-correlation coefficient (NSC) 1.073407 
Relative Strand cross-correlation Coefficient (RSC) 0.9576173 
Phantom Peak Quality Tag 0 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3

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, SRR1370879_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370879_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370879_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/SRR1370879_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/SRR1370879_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 29021.SRR1370879_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