BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161110_171002_928
Start time 2016-11-10 17:10:02
Run time 2 days 19:57:27.059
Tasks executed 8
Tasks failed 2
Tasks failed names 
spr rep1
dedup_bam_2 ctl1
Arguments* [-title, SRR1370885_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370885_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 0
* 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_171002_928_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10
chipseq.bds.20161110_171002_928_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_13
chipseq.bds.20161110_171002_928_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
thread_41 thread_Root 
 chipseq.bds.20161110_171002_928_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_11
chipseq.bds.20161110_171002_928_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_12
chipseq.bds.20161110_171002_928_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_14
chipseq.bds.20161110_171002_928_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_16
chipseq.bds.20161110_171002_928_parallel_41/task.postalign_bed.spr_rep1.line_255.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 6893
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 4
Mem
Start 2016-11-10 17:10:04
End 2016-11-10 17:28:53
Elapsed 00:18:48
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/SRR1370885_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/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_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/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_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/SRR1370885_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--------------------
30451 (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 6894
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 1
Mem
Start 2016-11-10 17:10:05
End 2016-11-10 17:19:15
Elapsed 00:09:09
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/rep1/SRR1370885_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/SRR1370885_1/out/align/rep1/SRR1370885_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/rep1/SRR1370885_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/rep1/SRR1370885_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--------------------
11026 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 17:10:23 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/rep1/SRR1370885_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 17:10:23 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 17:10:24	MarkDuplicates	Start of doWork freeMemory: 254878024; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 17:10:24	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 17:10:24	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 17:10:33	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position: chr1:165,325,912
INFO	2016-11-10 17:10:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:40	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    7s.  Last read position: chr2:103,631,972
INFO	2016-11-10 17:10:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:48	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    7s.  Last read position: chr3:111,034,059
INFO	2016-11-10 17:10:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:10:56	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    7s.  Last read position: chr5:4,003,924
INFO	2016-11-10 17:10:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:11:03	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    7s.  Last read position: chr5:178,547,286
INFO	2016-11-10 17:11:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:11:14	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:   10s.  Last read position: chr7:2,577,068
INFO	2016-11-10 17:11:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:11:22	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    8s.  Last read position: chr8:55,694,805
INFO	2016-11-10 17:11:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:11:30	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    8s.  Last read position: chr10:22,244,052
INFO	2016-11-10 17:11:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:11:39	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    8s.  Last read position: chr11:69,764,373
INFO	2016-11-10 17:11:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:11:48	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    8s.  Last read position: chr12:121,626,312
INFO	2016-11-10 17:11:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:11:59	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:   11s.  Last read position: chr15:63,169,945
INFO	2016-11-10 17:11:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:12:09	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    9s.  Last read position: chr17:16,360,241
INFO	2016-11-10 17:12:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:12:18	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    9s.  Last read position: chr19:8,610,459
INFO	2016-11-10 17:12:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:12:30	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:   12s.  Last read position: chr21:17,819,135
INFO	2016-11-10 17:12:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:12:39	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    8s.  Last read position: chrX:113,956,832
INFO	2016-11-10 17:12:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 17:12:42	MarkDuplicates	Read 15244872 records. 0 pairs never matched.
INFO	2016-11-10 17:12:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1744298992; totalMemory: 3104833536; maxMemory: 11453595648
INFO	2016-11-10 17:12:49	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 17:12:55	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 17:12:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 17:12:57	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 17:13:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 3072715280; totalMemory: 5968494592; maxMemory: 11453595648
INFO	2016-11-10 17:13:00	MarkDuplicates	Marking 864150 records as duplicates.
INFO	2016-11-10 17:13:00	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-10 17:17:00	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:04:00s.  Time for last 10,000,000:  240s.  Last read position: chr12:121,626,312
INFO	2016-11-10 17:19:13	MarkDuplicates	Before output close freeMemory: 5942473824; totalMemory: 5980553216; maxMemory: 11453595648
INFO	2016-11-10 17:19:13	MarkDuplicates	After output close freeMemory: 6201995224; totalMemory: 6240075776; maxMemory: 11453595648
[Thu Nov 10 17:19:13 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.84 minutes.
Runtime.totalMemory()=6240075776
Num 3
ID task.postalign_bam.dedup_bam_2_rep1.line_144.id_12
Name dedup_bam_2 rep1
Thread thread_41
PID 7149
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 17:19:16
End 2016-11-10 19:54:24
Elapsed 02:35:07
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.dupmark.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/rep1/SRR1370885_1.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/rep1/SRR1370885_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/SRR1370885_1/out/align/rep1/SRR1370885_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/rep1/SRR1370885_1.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_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/SRR1370885_1/out/qc/rep1/SRR1370885_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--------------------
18795 (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 7152
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 1
Mem
Start 2016-11-10 17:28:54
End 2016-11-10 20:28:55
Elapsed 03:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_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/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_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/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_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--------------------
56929 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 19:46:23 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_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 19:46:23 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 19:46:23	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 19:46:23	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 19:46:23	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 19:46:40	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:   12s.  Last read position: chr1:22,298,551
INFO	2016-11-10 19:46:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:46:48	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    8s.  Last read position: chr1:41,895,424
INFO	2016-11-10 19:46:48	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:46:59	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:   10s.  Last read position: chr1:63,396,527
INFO	2016-11-10 19:46:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:47:05	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    6s.  Last read position: chr1:89,147,707
INFO	2016-11-10 19:47:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:47:11	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    6s.  Last read position: chr1:115,615,553
INFO	2016-11-10 19:47:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:47:21	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    9s.  Last read position: chr1:164,468,682
INFO	2016-11-10 19:47:21	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:47:32	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:   10s.  Last read position: chr1:189,102,252
INFO	2016-11-10 19:47:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:47:37	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    5s.  Last read position: chr1:213,979,760
INFO	2016-11-10 19:47:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:47:50	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:   13s.  Last read position: chr1:231,814,268
INFO	2016-11-10 19:47:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:48:00	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    9s.  Last read position: chr2:3,652,468
INFO	2016-11-10 19:48:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:48:04	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    4s.  Last read position: chr2:39,505,122
INFO	2016-11-10 19:48:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:48:13	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    8s.  Last read position: chr2:73,561,393
INFO	2016-11-10 19:48:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:48:24	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:   11s.  Last read position: chr2:120,526,571
INFO	2016-11-10 19:48:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:48:33	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    8s.  Last read position: chr2:160,316,783
INFO	2016-11-10 19:48:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:48:37	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    4s.  Last read position: chr2:195,549,735
INFO	2016-11-10 19:48:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:48:44	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    7s.  Last read position: chr2:230,358,034
INFO	2016-11-10 19:48:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:48:54	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    9s.  Last read position: chr3:16,305,780
INFO	2016-11-10 19:48:54	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:48:59	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    4s.  Last read position: chr3:49,251,279
INFO	2016-11-10 19:48:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:03	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    4s.  Last read position: chr3:84,621,225
INFO	2016-11-10 19:49:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:09	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    6s.  Last read position: chr3:128,121,129
INFO	2016-11-10 19:49:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:21	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:   12s.  Last read position: chr3:165,373,238
INFO	2016-11-10 19:49:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:27	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    6s.  Last read position: chr3:195,333,247
INFO	2016-11-10 19:49:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:31	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:04s.  Time for last 1,000,000:    4s.  Last read position: chr4:37,752,582
INFO	2016-11-10 19:49:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:37	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    5s.  Last read position: chr4:81,286,306
INFO	2016-11-10 19:49:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:48	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:   11s.  Last read position: chr4:119,339,736
INFO	2016-11-10 19:49:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:55	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    6s.  Last read position: chr4:158,818,783
INFO	2016-11-10 19:49:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:50:00	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    5s.  Last read position: chr5:6,447,551
INFO	2016-11-10 19:50:00	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 19:50:06	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    6s.  Last read position: chr5:33,219,021
INFO	2016-11-10 19:50:06	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:50:13	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    6s.  Last read position: chr5:60,694,078
INFO	2016-11-10 19:50:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:50:24	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:   11s.  Last read position: chr5:86,336,676
INFO	2016-11-10 19:50:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:29	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    5s.  Last read position: chr5:112,930,184
INFO	2016-11-10 19:50:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:50:35	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    5s.  Last read position: chr5:136,852,889
INFO	2016-11-10 19:50:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:40	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    5s.  Last read position: chr5:160,271,193
INFO	2016-11-10 19:50:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:46	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    5s.  Last read position: chr6:4,126,386
INFO	2016-11-10 19:50:46	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:50:53	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    6s.  Last read position: chr6:28,666,579
INFO	2016-11-10 19:50:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:06	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:   13s.  Last read position: chr6:49,527,281
INFO	2016-11-10 19:51:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:10	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    4s.  Last read position: chr6:81,728,195
INFO	2016-11-10 19:51:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:19	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:51s.  Time for last 1,000,000:    8s.  Last read position: chr6:107,535,760
INFO	2016-11-10 19:51:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:23	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:55s.  Time for last 1,000,000:    4s.  Last read position: chr6:132,364,408
INFO	2016-11-10 19:51:23	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:51:31	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    8s.  Last read position: chr6:156,918,595
INFO	2016-11-10 19:51:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:45	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:   13s.  Last read position: chr7:18,636,743
INFO	2016-11-10 19:51:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:51	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    6s.  Last read position: chr7:53,850,313
INFO	2016-11-10 19:51:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:55	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    4s.  Last read position: chr7:96,503,433
INFO	2016-11-10 19:51:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:02	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    6s.  Last read position: chr7:120,651,846
INFO	2016-11-10 19:52:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:46	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:06:18s.  Time for last 1,000,000:   43s.  Last read position: chr7:146,401,497
INFO	2016-11-10 19:52:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:51	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    5s.  Last read position: chr8:17,030,519
INFO	2016-11-10 19:52:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:58	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    6s.  Last read position: chr8:42,750,671
INFO	2016-11-10 19:52:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:08	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:   10s.  Last read position: chr8:85,385,487
INFO	2016-11-10 19:53:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:15	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:    6s.  Last read position: chr8:124,358,985
INFO	2016-11-10 19:53:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:20	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    5s.  Last read position: chr9:18,183,883
INFO	2016-11-10 19:53:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:25	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    4s.  Last read position: chr9:84,163,983
INFO	2016-11-10 19:53:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:30	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    5s.  Last read position: chr9:119,875,535
INFO	2016-11-10 19:53:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:35	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    4s.  Last read position: chr10:5,661,683
INFO	2016-11-10 19:53:35	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:53:39	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    4s.  Last read position: chr10:29,748,948
INFO	2016-11-10 19:53:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:49	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    9s.  Last read position: chr10:61,280,221
INFO	2016-11-10 19:53:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:54	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    5s.  Last read position: chr10:85,305,552
INFO	2016-11-10 19:53:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:54:00	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    5s.  Last read position: chr10:108,129,202
INFO	2016-11-10 19:54:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:05	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    5s.  Last read position: chr10:132,730,123
INFO	2016-11-10 19:54:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:10	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:07:42s.  Time for last 1,000,000:    4s.  Last read position: chr11:35,359,267
INFO	2016-11-10 19:54:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:14	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    4s.  Last read position: chr11:75,696,431
INFO	2016-11-10 19:54:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:19	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    5s.  Last read position: chr11:114,414,621
INFO	2016-11-10 19:54:19	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:54:32	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:   13s.  Last read position: chr12:8,900,276
INFO	2016-11-10 19:54:32	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:54:38	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:08:10s.  Time for last 1,000,000:    5s.  Last read position: chr12:38,863,889
INFO	2016-11-10 19:54:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:42	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    4s.  Last read position: chr12:60,598,824
INFO	2016-11-10 19:54:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:47	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:08:19s.  Time for last 1,000,000:    4s.  Last read position: chr12:88,520,538
INFO	2016-11-10 19:54:47	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:54:52	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:08:24s.  Time for last 1,000,000:    5s.  Last read position: chr12:112,268,437
INFO	2016-11-10 19:54:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:00	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:08:33s.  Time for last 1,000,000:    8s.  Last read position: chr13:23,999,632
INFO	2016-11-10 19:55:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:06	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:08:39s.  Time for last 1,000,000:    5s.  Last read position: chr13:51,165,870
INFO	2016-11-10 19:55:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:12	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    5s.  Last read position: chr13:88,986,369
INFO	2016-11-10 19:55:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:16	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:08:48s.  Time for last 1,000,000:    4s.  Last read position: chr14:23,149,367
INFO	2016-11-10 19:55:16	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:55:21	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    5s.  Last read position: chr14:58,140,905
INFO	2016-11-10 19:55:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:26	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    4s.  Last read position: chr14:91,912,553
INFO	2016-11-10 19:55:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:38	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:09:10s.  Time for last 1,000,000:   11s.  Last read position: chr15:38,895,095
INFO	2016-11-10 19:55:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:46	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:09:18s.  Time for last 1,000,000:    7s.  Last read position: chr15:68,188,367
INFO	2016-11-10 19:55:46	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:55:52	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:09:25s.  Time for last 1,000,000:    6s.  Last read position: chr15:87,921,272
INFO	2016-11-10 19:55:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:00	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    7s.  Last read position: chr16:11,143,813
INFO	2016-11-10 19:56:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:07	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    7s.  Last read position: chr16:51,391,437
INFO	2016-11-10 19:56:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:56:25	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:   17s.  Last read position: chr16:84,928,458
INFO	2016-11-10 19:56:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:31	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:10:03s.  Time for last 1,000,000:    6s.  Last read position: chr17:18,368,935
INFO	2016-11-10 19:56:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:41	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:10:13s.  Time for last 1,000,000:    9s.  Last read position: chr17:44,246,522
INFO	2016-11-10 19:56:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:47	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    5s.  Last read position: chr17:66,172,158
INFO	2016-11-10 19:56:47	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 19:56:54	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:10:26s.  Time for last 1,000,000:    7s.  Last read position: chr18:5,619,614
INFO	2016-11-10 19:56:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:03	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    9s.  Last read position: chr18:46,152,631
INFO	2016-11-10 19:57:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:08	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:10:41s.  Time for last 1,000,000:    5s.  Last read position: chr19:1,328,731
INFO	2016-11-10 19:57:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:15	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:10:47s.  Time for last 1,000,000:    6s.  Last read position: chr19:28,148,444
INFO	2016-11-10 19:57:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:30	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:11:02s.  Time for last 1,000,000:   15s.  Last read position: chr19:40,341,579
INFO	2016-11-10 19:57:30	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:57:37	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:11:10s.  Time for last 1,000,000:    7s.  Last read position: chr20:3,222,035
INFO	2016-11-10 19:57:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:43	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:11:16s.  Time for last 1,000,000:    5s.  Last read position: chr20:37,218,903
INFO	2016-11-10 19:57:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:25	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:   41s.  Last read position: chr20:62,871,367
INFO	2016-11-10 19:58:25	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 19:58:34	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:12:06s.  Time for last 1,000,000:    9s.  Last read position: chr21:39,474,524
INFO	2016-11-10 19:58:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:42	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:12:14s.  Time for last 1,000,000:    7s.  Last read position: chr22:31,346,944
INFO	2016-11-10 19:58:42	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:48	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:12:21s.  Time for last 1,000,000:    6s.  Last read position: chrX:6,235,951
INFO	2016-11-10 19:58:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:58:57	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    8s.  Last read position: chrX:38,820,975
INFO	2016-11-10 19:58:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:03	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    5s.  Last read position: chrX:69,473,954
INFO	2016-11-10 19:59:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:10	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:12:42s.  Time for last 1,000,000:    7s.  Last read position: chrX:92,683,143
INFO	2016-11-10 19:59:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:16	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:12:49s.  Time for last 1,000,000:    6s.  Last read position: chrX:118,447,518
INFO	2016-11-10 19:59:16	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:59:26	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:12:58s.  Time for last 1,000,000:    9s.  Last read position: chrX:142,819,613
INFO	2016-11-10 19:59:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:59:32	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:13:04s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,995
INFO	2016-11-10 19:59:32	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 19:59:39	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:13:11s.  Time for last 1,000,000:    7s.  Last read position: chrM:11,775
INFO	2016-11-10 19:59:39	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 19:59:43	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 19:59:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 5962190616; totalMemory: 6036127744; maxMemory: 11453595648
INFO	2016-11-10 19:59:51	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 19:59:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 20:00:12	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 20:00:34	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 20:00:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5717823624; totalMemory: 8657043456; maxMemory: 11453595648
INFO	2016-11-10 20:00:35	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 20:00:35	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-10 20:02:55	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:20s.  Time for last 10,000,000:  140s.  Last read position: chr2:3,652,468
INFO	2016-11-10 20:05:26	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:51s.  Time for last 10,000,000:  150s.  Last read position: chr3:128,121,129
INFO	2016-11-10 20:08:04	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:07:29s.  Time for last 10,000,000:  158s.  Last read position: chr5:86,336,676
INFO	2016-11-10 20:10:55	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:10:20s.  Time for last 10,000,000:  171s.  Last read position: chr6:156,918,595
INFO	2016-11-10 20:13:50	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:13:14s.  Time for last 10,000,000:  174s.  Last read position: chr9:18,183,883
INFO	2016-11-10 20:16:46	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:16:11s.  Time for last 10,000,000:  176s.  Last read position: chr11:75,696,431
INFO	2016-11-10 20:19:43	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:19:08s.  Time for last 10,000,000:  176s.  Last read position: chr14:23,149,367
INFO	2016-11-10 20:22:45	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:22:10s.  Time for last 10,000,000:  182s.  Last read position: chr17:44,246,522
INFO	2016-11-10 20:25:57	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:25:21s.  Time for last 10,000,000:  191s.  Last read position: chr21:39,474,524
INFO	2016-11-10 20:28:53	MarkDuplicates	Before output close freeMemory: 9033126400; totalMemory: 9118416896; maxMemory: 11453595648
INFO	2016-11-10 20:28:53	MarkDuplicates	After output close freeMemory: 9033649632; totalMemory: 9118941184; maxMemory: 11453595648
[Thu Nov 10 20:28:53 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 42.51 minutes.
Runtime.totalMemory()=9118941184
Num 5
ID task.postalign_bam.bam_to_tag_rep1.line_505.id_14
Name bam_to_tag rep1
Thread thread_41
PID 7309
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 19:54:26
End 2016-11-10 20:55:48
Elapsed 01:01:22
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_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/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_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--------------------
53206 (process ID) old priority 0, new priority 10
Num 6
ID task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
Name dedup_bam_2 ctl1
Thread thread_42
PID 7360
OK false
Exit Code 3
Retries
State RUNNING
Dep. WAIT
Cpus 4
Mem
Start 2016-11-10 20:28:56
End 2016-11-10 20:28:56
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/ctl1/ss_50M_2000_GRCh38.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/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/ctl1/ss_50M_2000_GRCh38.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/SRR1370885_1/out/qc/ctl1/ss_50M_2000_GRCh38.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--------------------
20059 (process ID) old priority 0, new priority 10
Num 7
ID task.postalign_bed.subsample_tag_rep1.line_45.id_16
Name subsample_tag rep1
Thread thread_41
PID 7397
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-10 20:55:49
End 2016-11-10 21:38:22
Elapsed 00:42:32
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_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/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_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--------------------
43283 (process ID) old priority 0, new priority 10
Waiting for 28 seconds.
Num 8
ID task.postalign_bed.spr_rep1.line_255.id_17
Name spr rep1
Thread thread_41
PID 7493
OK false
Exit Code 3
Retries
State KILLED
Dep. ERROR
Cpus
Mem
Start 2016-11-10 21:38:25
End 2016-11-10 21:43:50
Elapsed 00:05:25
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr2/SRR1370885_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/SRR1370885_1/out/align/rep1/SRR1370885_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/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370885_1/out/align/pseudo_reps/rep1/pr1/SRR1370885_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--------------------
1603 (process ID) old priority 0, new priority 10
Waiting for 16 seconds.

Global scope

Note: Global scope when program finished execution.
Type Name Value
int{} filesize {rep1=3118379073, ctl1=11033042636}
int{} nth_rep {rep1=1, ctl1=4}