Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161110_170959_010
Start time	2016-11-10 17:09:59
Run time	07:15:59.299
Tasks executed	6
Tasks failed	0
Tasks failed names
Arguments*	[-title, SRR1370883_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370883_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

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20161110_170959_010/task.graphviz.report.line_97.id_14 chipseq.bds.20161110_170959_010/task.report.pdf2png.line_324.id_19
thread_41	thread_Root
thread_42	thread_Root	chipseq.bds.20161110_170959_010_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161110_170959_010_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_11 chipseq.bds.20161110_170959_010_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_12 chipseq.bds.20161110_170959_010_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_13

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	6890

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2016-11-10 17:10:00
End	2016-11-10 17:31:28
Elapsed	00:21:28
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/SRR1370883_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/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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/SRR1370883_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--------------------
14002 (process ID) old priority 0, new priority 10

Num	2
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_11
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	7155

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-11-10 17:31:30
End	2016-11-10 21:17:46
Elapsed	03:46:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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--------------------
47118 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 19:49:07 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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 19:49:07 PST 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-10 19:49:07	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 19:49:07	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 19:49:07	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: 00:00:09s.  Time for last 1,000,000:    9s.  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 19:49:28	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    8s.  Last read position: chr1:41,895,424
INFO	2016-11-10 19:49:28	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:49:36	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    8s.  Last read position: chr1:63,396,527
INFO	2016-11-10 19:49:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:49:45	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    9s.  Last read position: chr1:89,147,707
INFO	2016-11-10 19:49:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:55	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    9s.  Last read position: chr1:115,615,553
INFO	2016-11-10 19:49:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:02	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    6s.  Last read position: chr1:164,468,682
INFO	2016-11-10 19:50:02	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:50:08	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    6s.  Last read position: chr1:189,102,252
INFO	2016-11-10 19:50:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:50:14	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    6s.  Last read position: chr1:213,979,760
INFO	2016-11-10 19:50:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:21	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    6s.  Last read position: chr1:231,814,268
INFO	2016-11-10 19:50:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:31	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    9s.  Last read position: chr2:3,652,468
INFO	2016-11-10 19:50:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:50:37	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    6s.  Last read position: chr2:39,505,122
INFO	2016-11-10 19:50:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:43	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    5s.  Last read position: chr2:73,561,393
INFO	2016-11-10 19:50:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:50:48	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    4s.  Last read position: chr2:120,526,571
INFO	2016-11-10 19:50:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:57	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    9s.  Last read position: chr2:160,316,783
INFO	2016-11-10 19:50:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:04	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    7s.  Last read position: chr2:195,549,735
INFO	2016-11-10 19:51:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:14	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:   10s.  Last read position: chr2:230,358,034
INFO	2016-11-10 19:51:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:51:19	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    4s.  Last read position: chr3:16,305,780
INFO	2016-11-10 19:51:19	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:51:24	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    5s.  Last read position: chr3:49,251,279
INFO	2016-11-10 19:51:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:34	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    9s.  Last read position: chr3:84,621,225
INFO	2016-11-10 19:51:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:44	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:   10s.  Last read position: chr3:128,121,129
INFO	2016-11-10 19:51:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:50	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    5s.  Last read position: chr3:165,373,238
INFO	2016-11-10 19:51:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:55	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    5s.  Last read position: chr3:195,333,247
INFO	2016-11-10 19:51:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:01	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    5s.  Last read position: chr4:37,752,582
INFO	2016-11-10 19:52:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:11	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:   10s.  Last read position: chr4:81,286,306
INFO	2016-11-10 19:52:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:15	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    4s.  Last read position: chr4:119,339,736
INFO	2016-11-10 19:52:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:22	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    6s.  Last read position: chr4:158,818,783
INFO	2016-11-10 19:52:22	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:52:29	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:    7s.  Last read position: chr5:6,447,551
INFO	2016-11-10 19:52:29	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 19:52:35	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    6s.  Last read position: chr5:33,219,021
INFO	2016-11-10 19:52:35	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:52:43	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    7s.  Last read position: chr5:60,694,078
INFO	2016-11-10 19:52:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:52:54	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:   11s.  Last read position: chr5:86,336,676
INFO	2016-11-10 19:52:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:59	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    5s.  Last read position: chr5:112,930,184
INFO	2016-11-10 19:52:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:03	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:53s.  Time for last 1,000,000:    3s.  Last read position: chr5:136,852,889
INFO	2016-11-10 19:53:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:10	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    6s.  Last read position: chr5:160,271,193
INFO	2016-11-10 19:53:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:16	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    6s.  Last read position: chr6:4,126,386
INFO	2016-11-10 19:53:16	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:53:29	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:   12s.  Last read position: chr6:28,666,579
INFO	2016-11-10 19:53:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:33	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    4s.  Last read position: chr6:49,527,281
INFO	2016-11-10 19:53:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:38	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    5s.  Last read position: chr6:81,728,195
INFO	2016-11-10 19:53:38	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:44	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:    5s.  Last read position: chr6:107,535,760
INFO	2016-11-10 19:53:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:50	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    6s.  Last read position: chr6:132,364,408
INFO	2016-11-10 19:53:50	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:53:55	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    4s.  Last read position: chr6:156,918,595
INFO	2016-11-10 19:53:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:09	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:   13s.  Last read position: chr7:18,636,743
INFO	2016-11-10 19:54:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:14	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    5s.  Last read position: chr7:53,850,313
INFO	2016-11-10 19:54:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:20	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    5s.  Last read position: chr7:96,503,433
INFO	2016-11-10 19:54:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:25	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    5s.  Last read position: chr7:120,651,846
INFO	2016-11-10 19:54:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:07	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:   41s.  Last read position: chr7:146,401,497
INFO	2016-11-10 19:55:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:15	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    7s.  Last read position: chr8:17,030,519
INFO	2016-11-10 19:55:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:20	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    5s.  Last read position: chr8:42,750,671
INFO	2016-11-10 19:55:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:26	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    5s.  Last read position: chr8:85,385,487
INFO	2016-11-10 19:55:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:31	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    4s.  Last read position: chr8:124,358,985
INFO	2016-11-10 19:55:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:40	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    9s.  Last read position: chr9:18,183,883
INFO	2016-11-10 19:55:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:47	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    6s.  Last read position: chr9:84,163,983
INFO	2016-11-10 19:55:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:56	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:    9s.  Last read position: chr9:119,875,535
INFO	2016-11-10 19:55:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:03	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    6s.  Last read position: chr10:5,661,683
INFO	2016-11-10 19:56:03	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:56:09	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    5s.  Last read position: chr10:29,748,948
INFO	2016-11-10 19:56:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:13	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    4s.  Last read position: chr10:61,280,221
INFO	2016-11-10 19:56:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:18	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:    5s.  Last read position: chr10:85,305,552
INFO	2016-11-10 19:56:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:56:25	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    6s.  Last read position: chr10:108,129,202
INFO	2016-11-10 19:56:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:29	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:07:20s.  Time for last 1,000,000:    4s.  Last read position: chr10:132,730,123
INFO	2016-11-10 19:56:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:41	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:   11s.  Last read position: chr11:35,359,267
INFO	2016-11-10 19:56:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:47	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:    5s.  Last read position: chr11:75,696,431
INFO	2016-11-10 19:56:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:51	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    4s.  Last read position: chr11:114,414,621
INFO	2016-11-10 19:56:51	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:57:00	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    8s.  Last read position: chr12:8,900,276
INFO	2016-11-10 19:57:00	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:57:06	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    6s.  Last read position: chr12:38,863,889
INFO	2016-11-10 19:57:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:18	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:   11s.  Last read position: chr12:60,598,824
INFO	2016-11-10 19:57:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:22	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    4s.  Last read position: chr12:88,520,538
INFO	2016-11-10 19:57:22	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:57:26	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    3s.  Last read position: chr12:112,268,437
INFO	2016-11-10 19:57:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:33	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    6s.  Last read position: chr13:23,999,632
INFO	2016-11-10 19:57:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:41	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    8s.  Last read position: chr13:51,165,870
INFO	2016-11-10 19:57:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:57:47	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    6s.  Last read position: chr13:88,986,369
INFO	2016-11-10 19:57:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:52	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    4s.  Last read position: chr14:23,149,367
INFO	2016-11-10 19:57:52	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:00	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:    7s.  Last read position: chr14:58,140,905
INFO	2016-11-10 19:58:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:04	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    4s.  Last read position: chr14:91,912,553
INFO	2016-11-10 19:58:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:58:22	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:09:12s.  Time for last 1,000,000:   18s.  Last read position: chr15:38,895,095
INFO	2016-11-10 19:58:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:27	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:09:18s.  Time for last 1,000,000:    5s.  Last read position: chr15:68,188,367
INFO	2016-11-10 19:58:27	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:39	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:09:30s.  Time for last 1,000,000:   11s.  Last read position: chr15:87,921,272
INFO	2016-11-10 19:58:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:45	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    5s.  Last read position: chr16:11,143,813
INFO	2016-11-10 19:58:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:49	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    4s.  Last read position: chr16:51,391,437
INFO	2016-11-10 19:58:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:59:02	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:09:52s.  Time for last 1,000,000:   12s.  Last read position: chr16:84,928,458
INFO	2016-11-10 19:59:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:08	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:09:58s.  Time for last 1,000,000:    6s.  Last read position: chr17:18,368,935
INFO	2016-11-10 19:59:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:14	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:10:04s.  Time for last 1,000,000:    5s.  Last read position: chr17:44,246,522
INFO	2016-11-10 19:59:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:20	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:10:10s.  Time for last 1,000,000:    5s.  Last read position: chr17:66,172,158
INFO	2016-11-10 19:59:20	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 19:59:25	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:10:15s.  Time for last 1,000,000:    5s.  Last read position: chr18:5,619,614
INFO	2016-11-10 19:59:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:43	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:10:33s.  Time for last 1,000,000:   17s.  Last read position: chr18:46,152,631
INFO	2016-11-10 19:59:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:54	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:10:44s.  Time for last 1,000,000:   11s.  Last read position: chr19:1,328,731
INFO	2016-11-10 19:59:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:00:00	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:10:50s.  Time for last 1,000,000:    5s.  Last read position: chr19:28,148,444
INFO	2016-11-10 20:00:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:00:05	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:10:55s.  Time for last 1,000,000:    5s.  Last read position: chr19:40,341,579
INFO	2016-11-10 20:00:05	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:00:10	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:11:00s.  Time for last 1,000,000:    4s.  Last read position: chr20:3,222,035
INFO	2016-11-10 20:00:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:00:18	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:11:08s.  Time for last 1,000,000:    8s.  Last read position: chr20:37,218,903
INFO	2016-11-10 20:00:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:03	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:11:53s.  Time for last 1,000,000:   45s.  Last read position: chr20:62,871,367
INFO	2016-11-10 20:01:03	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 20:01:08	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:11:58s.  Time for last 1,000,000:    5s.  Last read position: chr21:39,474,524
INFO	2016-11-10 20:01:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:15	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:12:05s.  Time for last 1,000,000:    6s.  Last read position: chr22:31,346,944
INFO	2016-11-10 20:01:15	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:01:19	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:12:10s.  Time for last 1,000,000:    4s.  Last read position: chrX:6,235,951
INFO	2016-11-10 20:01:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:01:25	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:    5s.  Last read position: chrX:38,820,975
INFO	2016-11-10 20:01:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:30	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:12:21s.  Time for last 1,000,000:    5s.  Last read position: chrX:69,473,954
INFO	2016-11-10 20:01:30	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:36	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:12:27s.  Time for last 1,000,000:    6s.  Last read position: chrX:92,683,143
INFO	2016-11-10 20:01:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:45	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    8s.  Last read position: chrX:118,447,518
INFO	2016-11-10 20:01:45	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:01:55	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:12:45s.  Time for last 1,000,000:   10s.  Last read position: chrX:142,819,613
INFO	2016-11-10 20:01:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:02:02	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,995
INFO	2016-11-10 20:02:02	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 20:02:10	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:13:00s.  Time for last 1,000,000:    7s.  Last read position: chrM:11,775
INFO	2016-11-10 20:02:10	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 20:02:21	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 20:02:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 6235360320; totalMemory: 6307708928; maxMemory: 11453595648
INFO	2016-11-10 20:02:29	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 20:02:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 20:02:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 20:03:22	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 20:03:23	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5952309128; totalMemory: 8889303040; maxMemory: 11453595648
INFO	2016-11-10 20:03:23	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 20:03:23	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-10 20:06:18	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:54s.  Time for last 10,000,000:  174s.  Last read position: chr2:3,652,468
INFO	2016-11-10 20:09:18	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:05:54s.  Time for last 10,000,000:  180s.  Last read position: chr3:128,121,129
INFO	2016-11-10 20:12:15	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:08:51s.  Time for last 10,000,000:  177s.  Last read position: chr5:86,336,676
INFO	2016-11-10 20:17:21	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:13:57s.  Time for last 10,000,000:  305s.  Last read position: chr6:156,918,595
INFO	2016-11-10 20:23:39	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:20:15s.  Time for last 10,000,000:  378s.  Last read position: chr9:18,183,883
INFO	2016-11-10 20:33:32	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:30:08s.  Time for last 10,000,000:  592s.  Last read position: chr11:75,696,431
INFO	2016-11-10 20:46:13	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:42:49s.  Time for last 10,000,000:  761s.  Last read position: chr14:23,149,367
INFO	2016-11-10 20:56:04	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:52:40s.  Time for last 10,000,000:  591s.  Last read position: chr17:44,246,522
INFO	2016-11-10 21:07:00	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 01:03:36s.  Time for last 10,000,000:  656s.  Last read position: chr21:39,474,524
INFO	2016-11-10 21:16:22	MarkDuplicates	Before output close freeMemory: 9280490504; totalMemory: 9364307968; maxMemory: 11453595648
INFO	2016-11-10 21:17:22	MarkDuplicates	After output close freeMemory: 9282586600; totalMemory: 9366405120; maxMemory: 11453595648
[Thu Nov 10 21:17:31 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 88.40 minutes.
Runtime.totalMemory()=9366405120

Num	3
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_12
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	7417

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2016-11-10 21:17:47
End	2016-11-11 00:13:36
Elapsed	02:55:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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/SRR1370883_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/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_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/SRR1370883_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/SRR1370883_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--------------------
23986 (process ID) old priority 0, new priority 10

Num	4
ID	task.postalign_bam.bam_to_tag_ctl1.line_505.id_13
Name	bam_to_tag ctl1
Thread	thread_42
PID	7947

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

Start	2016-11-11 00:13:38
End	2016-11-11 00:25:48
Elapsed	00:12:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 507

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

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

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

   
--------------------Stdout--------------------
44330 (process ID) old priority 0, new priority 10

Num	5
ID	task.graphviz.report.line_97.id_14
Name	report
Thread	thread_Root
PID	7262

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

Start	2016-11-11 00:25:49
End	2016-11-11 00:25:57
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 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 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/report/SRR1370883_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/report/SRR1370883_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/report/SRR1370883_1_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
7266 (process ID) old priority 0, new priority 10

Num	6
ID	task.report.pdf2png.line_324.id_19
Name	pdf2png
Thread	thread_Root
PID	7298

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

Start	2016-11-11 00:25:49
End	2016-11-11 00:25:58
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/qc/rep1/SRR1370883_1.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/qc/rep1/SRR1370883_1.nodup.15M.cc.plot.png
Dependencies

 
# SYS command. line 325

 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 326

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/qc/rep1/SRR1370883_1.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out/qc/rep1/SRR1370883_1.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
7303 (process ID) old priority 0, new priority 10

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, SRR1370883_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370883_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370883_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/SRR1370883_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/SRR1370883_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	29492.SRR1370883_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

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope