Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161113_215907_032
Start time	2016-11-13 21:59:07
Run time	04:15:14.791
Tasks executed	15
Tasks failed	0
Tasks failed names
Arguments*	[-title, SRR1370905_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_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.20161113_215907_032/task.graphviz.report.line_97.id_23 chipseq.bds.20161113_215907_032/task.report.pdf2png.line_324.id_28
thread_41	thread_Root	chipseq.bds.20161113_215907_032_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161113_215907_032_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 chipseq.bds.20161113_215907_032_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_14 chipseq.bds.20161113_215907_032_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_16 chipseq.bds.20161113_215907_032_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_17 chipseq.bds.20161113_215907_032_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_18 chipseq.bds.20161113_215907_032_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_19 chipseq.bds.20161113_215907_032_parallel_41/task.postalign_bed.spr_rep1.line_255.id_20 chipseq.bds.20161113_215907_032_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_21
thread_42	thread_Root	chipseq.bds.20161113_215907_032_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 chipseq.bds.20161113_215907_032_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 chipseq.bds.20161113_215907_032_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20161113_215907_032_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_22

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bwa.bwa_aln_rep1.line_108.id_10
Name	bwa_aln rep1
Thread	thread_41
PID	10248

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

Start	2016-11-13 21:59:09
End	2016-11-13 22:44:08
Elapsed	00:44:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.sai
Dependencies

 
# SYS command. line 110

 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 113

 bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.sai

# SYS command. line 115

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

   
--------------------Stdout--------------------
14908 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.35 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.79 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.51 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.78 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.93 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.77 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13308961 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz
[main] Real time: 2688.524 sec; CPU: 2662.656 sec

Num	2
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	10249

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

Start	2016-11-13 21:59:09
End	2016-11-13 22:20:39
Elapsed	00:21:30
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/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_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--------------------
11063 (process ID) old priority 0, new priority 10

Num	3
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	10505

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

Start	2016-11-13 22:20:41
End	2016-11-13 23:35:59
Elapsed	01:15:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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--------------------
10965 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Nov 13 22:41:36 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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
[Sun Nov 13 22:41:36 PST 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-13 22:41:36	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-13 22:41:36	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-13 22:41:36	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-13 22:41:47	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:   10s.  Last read position: chr1:22,298,551
INFO	2016-11-13 22:41:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:41:55	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	2016-11-13 22:41:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:42:04	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    8s.  Last read position: chr1:63,396,527
INFO	2016-11-13 22:42:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:42:12	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    7s.  Last read position: chr1:89,147,707
INFO	2016-11-13 22:42:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:42:20	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    8s.  Last read position: chr1:115,615,553
INFO	2016-11-13 22:42:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:42:31	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:   11s.  Last read position: chr1:164,468,682
INFO	2016-11-13 22:42:31	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 22:42:38	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    7s.  Last read position: chr1:189,102,252
INFO	2016-11-13 22:42:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:42:48	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    9s.  Last read position: chr1:213,979,760
INFO	2016-11-13 22:42:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:42:58	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   10s.  Last read position: chr1:231,814,268
INFO	2016-11-13 22:42:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:43:06	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:    7s.  Last read position: chr2:3,652,468
INFO	2016-11-13 22:43:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:43:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    7s.  Last read position: chr2:39,505,122
INFO	2016-11-13 22:43:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:43:25	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:   11s.  Last read position: chr2:73,561,393
INFO	2016-11-13 22:43:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:43:35	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    9s.  Last read position: chr2:120,526,571
INFO	2016-11-13 22:43:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:43:45	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:   10s.  Last read position: chr2:160,316,783
INFO	2016-11-13 22:43:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:43:56	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:   10s.  Last read position: chr2:195,549,735
INFO	2016-11-13 22:43:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:44:16	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:   19s.  Last read position: chr2:230,358,034
INFO	2016-11-13 22:44:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:44:34	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:   18s.  Last read position: chr3:16,305,780
INFO	2016-11-13 22:44:34	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 22:44:42	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    8s.  Last read position: chr3:49,251,279
INFO	2016-11-13 22:44:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:44:51	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    8s.  Last read position: chr3:84,621,225
INFO	2016-11-13 22:44:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:45:00	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    8s.  Last read position: chr3:128,121,129
INFO	2016-11-13 22:45:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:45:09	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    9s.  Last read position: chr3:165,373,238
INFO	2016-11-13 22:45:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:45:17	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    8s.  Last read position: chr3:195,333,247
INFO	2016-11-13 22:45:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:45:25	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    7s.  Last read position: chr4:37,752,582
INFO	2016-11-13 22:45:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:45:40	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:   15s.  Last read position: chr4:81,286,306
INFO	2016-11-13 22:45:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:45:56	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:   16s.  Last read position: chr4:119,339,736
INFO	2016-11-13 22:45:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:46:06	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    9s.  Last read position: chr4:158,818,783
INFO	2016-11-13 22:46:06	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:46:15	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    9s.  Last read position: chr5:6,447,551
INFO	2016-11-13 22:46:15	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-13 22:46:24	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:    8s.  Last read position: chr5:33,219,021
INFO	2016-11-13 22:46:24	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 22:46:32	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    8s.  Last read position: chr5:60,694,078
INFO	2016-11-13 22:46:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:46:41	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    8s.  Last read position: chr5:86,336,676
INFO	2016-11-13 22:46:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:46:57	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:   15s.  Last read position: chr5:112,930,184
INFO	2016-11-13 22:46:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:47:06	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    9s.  Last read position: chr5:136,852,889
INFO	2016-11-13 22:47:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:47:14	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    7s.  Last read position: chr5:160,271,193
INFO	2016-11-13 22:47:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:47:23	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    8s.  Last read position: chr6:4,126,386
INFO	2016-11-13 22:47:23	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 22:47:32	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    8s.  Last read position: chr6:28,666,579
INFO	2016-11-13 22:47:32	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:47:39	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    7s.  Last read position: chr6:49,527,281
INFO	2016-11-13 22:47:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:47:49	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    9s.  Last read position: chr6:81,728,195
INFO	2016-11-13 22:47:49	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:47:58	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    8s.  Last read position: chr6:107,535,760
INFO	2016-11-13 22:47:58	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:48:06	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    7s.  Last read position: chr6:132,364,408
INFO	2016-11-13 22:48:06	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:48:15	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    9s.  Last read position: chr6:156,918,595
INFO	2016-11-13 22:48:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:48:27	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:   12s.  Last read position: chr7:18,636,743
INFO	2016-11-13 22:48:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:48:41	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:   13s.  Last read position: chr7:53,850,313
INFO	2016-11-13 22:48:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:49:10	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:   29s.  Last read position: chr7:96,503,433
INFO	2016-11-13 22:49:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:49:24	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:   13s.  Last read position: chr7:120,651,846
INFO	2016-11-13 22:49:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:50:19	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:08:43s.  Time for last 1,000,000:   55s.  Last read position: chr7:146,401,497
INFO	2016-11-13 22:50:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:50:28	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    8s.  Last read position: chr8:17,030,519
INFO	2016-11-13 22:50:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:50:46	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:   17s.  Last read position: chr8:42,750,671
INFO	2016-11-13 22:50:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:50:53	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    7s.  Last read position: chr8:85,385,487
INFO	2016-11-13 22:50:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:51:03	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:09:27s.  Time for last 1,000,000:    9s.  Last read position: chr8:124,358,985
INFO	2016-11-13 22:51:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:51:11	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    7s.  Last read position: chr9:18,183,883
INFO	2016-11-13 22:51:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:51:19	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:    7s.  Last read position: chr9:84,163,983
INFO	2016-11-13 22:51:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:51:26	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    7s.  Last read position: chr9:119,875,535
INFO	2016-11-13 22:51:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:51:36	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:    9s.  Last read position: chr10:5,661,683
INFO	2016-11-13 22:51:36	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:51:44	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:10:07s.  Time for last 1,000,000:    8s.  Last read position: chr10:29,748,948
INFO	2016-11-13 22:51:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:51:54	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:10:18s.  Time for last 1,000,000:   10s.  Last read position: chr10:61,280,221
INFO	2016-11-13 22:51:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:52:02	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:10:26s.  Time for last 1,000,000:    8s.  Last read position: chr10:85,305,552
INFO	2016-11-13 22:52:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:52:12	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    9s.  Last read position: chr10:108,129,202
INFO	2016-11-13 22:52:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:52:22	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:10:45s.  Time for last 1,000,000:    9s.  Last read position: chr10:132,730,123
INFO	2016-11-13 22:52:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:52:29	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:10:53s.  Time for last 1,000,000:    7s.  Last read position: chr11:35,359,267
INFO	2016-11-13 22:52:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:53:00	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:11:23s.  Time for last 1,000,000:   30s.  Last read position: chr11:75,696,431
INFO	2016-11-13 22:53:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:53:19	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:11:43s.  Time for last 1,000,000:   19s.  Last read position: chr11:114,414,621
INFO	2016-11-13 22:53:19	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 22:53:28	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:11:51s.  Time for last 1,000,000:    8s.  Last read position: chr12:8,900,276
INFO	2016-11-13 22:53:28	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:53:37	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:    9s.  Last read position: chr12:38,863,889
INFO	2016-11-13 22:53:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:53:45	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:12:09s.  Time for last 1,000,000:    8s.  Last read position: chr12:60,598,824
INFO	2016-11-13 22:53:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:54:03	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:12:27s.  Time for last 1,000,000:   17s.  Last read position: chr12:88,520,538
INFO	2016-11-13 22:54:03	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 22:54:11	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    7s.  Last read position: chr12:112,268,437
INFO	2016-11-13 22:54:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:54:20	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:12:43s.  Time for last 1,000,000:    8s.  Last read position: chr13:23,999,632
INFO	2016-11-13 22:54:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:54:31	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:   11s.  Last read position: chr13:51,165,870
INFO	2016-11-13 22:54:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:54:39	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:13:03s.  Time for last 1,000,000:    7s.  Last read position: chr13:88,986,369
INFO	2016-11-13 22:54:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:54:48	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:13:12s.  Time for last 1,000,000:    8s.  Last read position: chr14:23,149,367
INFO	2016-11-13 22:54:48	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:54:58	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:13:22s.  Time for last 1,000,000:   10s.  Last read position: chr14:58,140,905
INFO	2016-11-13 22:54:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:55:08	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:13:31s.  Time for last 1,000,000:    9s.  Last read position: chr14:91,912,553
INFO	2016-11-13 22:55:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:55:18	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:13:41s.  Time for last 1,000,000:    9s.  Last read position: chr15:38,895,095
INFO	2016-11-13 22:55:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:55:29	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:13:53s.  Time for last 1,000,000:   11s.  Last read position: chr15:68,188,367
INFO	2016-11-13 22:55:29	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:55:40	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:14:04s.  Time for last 1,000,000:   11s.  Last read position: chr15:87,921,272
INFO	2016-11-13 22:55:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:56:12	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:14:36s.  Time for last 1,000,000:   32s.  Last read position: chr16:11,143,813
INFO	2016-11-13 22:56:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:56:24	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:14:47s.  Time for last 1,000,000:   11s.  Last read position: chr16:51,391,437
INFO	2016-11-13 22:56:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:56:34	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:14:58s.  Time for last 1,000,000:   10s.  Last read position: chr16:84,928,458
INFO	2016-11-13 22:56:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:56:45	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:15:08s.  Time for last 1,000,000:   10s.  Last read position: chr17:18,368,935
INFO	2016-11-13 22:56:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:56:53	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:15:16s.  Time for last 1,000,000:    7s.  Last read position: chr17:44,246,522
INFO	2016-11-13 22:56:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:57:00	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:15:24s.  Time for last 1,000,000:    7s.  Last read position: chr17:66,172,158
INFO	2016-11-13 22:57:00	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-13 22:57:11	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:15:35s.  Time for last 1,000,000:   11s.  Last read position: chr18:5,619,614
INFO	2016-11-13 22:57:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:57:20	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:15:43s.  Time for last 1,000,000:    8s.  Last read position: chr18:46,152,631
INFO	2016-11-13 22:57:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:57:28	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:15:51s.  Time for last 1,000,000:    7s.  Last read position: chr19:1,328,731
INFO	2016-11-13 22:57:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:57:37	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:16:00s.  Time for last 1,000,000:    8s.  Last read position: chr19:28,148,444
INFO	2016-11-13 22:57:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:58:01	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:16:25s.  Time for last 1,000,000:   24s.  Last read position: chr19:40,341,579
INFO	2016-11-13 22:58:01	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 22:58:10	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:16:33s.  Time for last 1,000,000:    8s.  Last read position: chr20:3,222,035
INFO	2016-11-13 22:58:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:58:19	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:16:42s.  Time for last 1,000,000:    9s.  Last read position: chr20:37,218,903
INFO	2016-11-13 22:58:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:59:03	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:17:27s.  Time for last 1,000,000:   44s.  Last read position: chr20:62,871,367
INFO	2016-11-13 22:59:03	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-13 22:59:12	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:17:35s.  Time for last 1,000,000:    8s.  Last read position: chr21:39,474,524
INFO	2016-11-13 22:59:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:59:19	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:17:43s.  Time for last 1,000,000:    7s.  Last read position: chr22:31,346,944
INFO	2016-11-13 22:59:19	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-13 22:59:27	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:17:50s.  Time for last 1,000,000:    7s.  Last read position: chrX:6,235,951
INFO	2016-11-13 22:59:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 22:59:34	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:17:58s.  Time for last 1,000,000:    7s.  Last read position: chrX:38,820,975
INFO	2016-11-13 22:59:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-13 22:59:41	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:18:04s.  Time for last 1,000,000:    6s.  Last read position: chrX:69,473,954
INFO	2016-11-13 22:59:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:59:51	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:18:14s.  Time for last 1,000,000:    9s.  Last read position: chrX:92,683,143
INFO	2016-11-13 22:59:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-13 22:59:59	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:18:23s.  Time for last 1,000,000:    8s.  Last read position: chrX:118,447,518
INFO	2016-11-13 22:59:59	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-13 23:00:13	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:18:36s.  Time for last 1,000,000:   13s.  Last read position: chrX:142,819,613
INFO	2016-11-13 23:00:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:00:22	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:18:46s.  Time for last 1,000,000:    9s.  Last read position: chrM:3,995
INFO	2016-11-13 23:00:22	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-13 23:00:34	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:18:57s.  Time for last 1,000,000:   11s.  Last read position: chrM:11,775
INFO	2016-11-13 23:00:34	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-13 23:00:47	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-13 23:00:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 5854175112; totalMemory: 5901385728; maxMemory: 11453595648
INFO	2016-11-13 23:00:56	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-13 23:00:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-13 23:01:23	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-13 23:02:00	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-13 23:02:01	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5964491688; totalMemory: 8880914432; maxMemory: 11453595648
INFO	2016-11-13 23:02:01	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-13 23:02:01	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-13 23:05:08	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:03:07s.  Time for last 10,000,000:  187s.  Last read position: chr2:3,652,468
INFO	2016-11-13 23:08:37	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:06:35s.  Time for last 10,000,000:  208s.  Last read position: chr3:128,121,129
INFO	2016-11-13 23:12:19	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:10:18s.  Time for last 10,000,000:  222s.  Last read position: chr5:86,336,676
INFO	2016-11-13 23:15:44	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:13:43s.  Time for last 10,000,000:  204s.  Last read position: chr6:156,918,595
INFO	2016-11-13 23:19:12	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:17:10s.  Time for last 10,000,000:  207s.  Last read position: chr9:18,183,883
INFO	2016-11-13 23:22:43	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:20:42s.  Time for last 10,000,000:  211s.  Last read position: chr11:75,696,431
INFO	2016-11-13 23:26:05	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:24:03s.  Time for last 10,000,000:  201s.  Last read position: chr14:23,149,367
INFO	2016-11-13 23:29:32	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:27:31s.  Time for last 10,000,000:  207s.  Last read position: chr17:44,246,522
INFO	2016-11-13 23:33:01	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:31:00s.  Time for last 10,000,000:  208s.  Last read position: chr21:39,474,524
INFO	2016-11-13 23:35:57	MarkDuplicates	Before output close freeMemory: 8630822584; totalMemory: 8696365056; maxMemory: 11453595648
INFO	2016-11-13 23:35:58	MarkDuplicates	After output close freeMemory: 8631345816; totalMemory: 8696889344; maxMemory: 11453595648
[Sun Nov 13 23:35:58 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 54.37 minutes.
Runtime.totalMemory()=8696889344

Num	4
ID	task.align_bwa.bwa_sam_rep1.line_140.id_13
Name	bwa_sam rep1
Thread	thread_41
PID	10579

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

Start	2016-11-13 22:44:10
End	2016-11-13 23:35:00
Elapsed	00:50:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.flagstat.qc
Dependencies

 
# SYS command. line 142

 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 147

 bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.flagstat.qc

# SYS command. line 151

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

   
--------------------Stdout--------------------
6118 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.49 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.51 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.16 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.33 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.61 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.53 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.94 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.97 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.12 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.30 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.70 sec
[bwa_aln_core] refine gapped alignments... 1.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.35 sec
[bwa_aln_core] refine gapped alignments... 2.02 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.29 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.10 sec
[bwa_aln_core] refine gapped alignments... 7.04 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.69 sec
[bwa_aln_core] refine gapped alignments... 3.19 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.40 sec
[bwa_aln_core] refine gapped alignments... 3.53 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.84 sec
[bwa_aln_core] refine gapped alignments... 4.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.55 sec
[bwa_aln_core] refine gapped alignments... 4.95 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.37 sec
[bwa_aln_core] refine gapped alignments... 6.59 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.13 sec
[bwa_aln_core] refine gapped alignments... 6.91 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.50 sec
[bwa_aln_core] refine gapped alignments... 6.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.30 sec
[bwa_aln_core] refine gapped alignments... 8.32 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.46 sec
[bwa_aln_core] refine gapped alignments... 8.98 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.74 sec
[bwa_aln_core] refine gapped alignments... 10.67 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.55 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.36 sec
[bwa_aln_core] refine gapped alignments... 5.18 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.97 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.89 sec
[bwa_aln_core] refine gapped alignments... 7.57 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.97 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.96 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.65 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.60 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.32 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.46 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.40 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.30 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.22 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.47 sec
[bwa_aln_core] refine gapped alignments... 2.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.70 sec
[bwa_aln_core] refine gapped alignments... 1.64 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.05 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.45 sec
[bwa_aln_core] refine gapped alignments... 1.64 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.39 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.81 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.42 sec
[bwa_aln_core] refine gapped alignments... 2.89 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.48 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.33 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.53 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.02 sec
[bwa_aln_core] refine gapped alignments... 2.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.87 sec
[bwa_aln_core] refine gapped alignments... 3.92 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 106.00 sec
[bwa_aln_core] refine gapped alignments... 7.54 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 13308961 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz
[main] Real time: 2281.623 sec; CPU: 2214.696 sec

Num	5
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_14
Name	dedup_bam_1 rep1
Thread	thread_41
PID	10818

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

Start	2016-11-13 23:35:02
End	2016-11-13 23:40:27
Elapsed	00:05:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.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 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.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--------------------
29016 (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	10825

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

Start	2016-11-13 23:36:00
End	2016-11-14 02:08:01
Elapsed	02:32:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_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/SRR1370905_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--------------------
34656 (process ID) old priority 0, new priority 10

Num	7
ID	task.postalign_bam.markdup_bam_picard_rep1.line_348.id_16
Name	markdup_bam_picard rep1
Thread	thread_41
PID	10854

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

Start	2016-11-13 23:40:28
End	2016-11-13 23:45:22
Elapsed	00:04:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_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/SRR1370905_1/out/align/rep1/SRR1370905_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_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--------------------
31282 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Nov 13 23:40:51 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Nov 13 23:40:51 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	2016-11-13 23:40:52	MarkDuplicates	Start of doWork freeMemory: 254879488; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-13 23:40:52	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-13 23:40:52	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-13 23:41:15	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:   16s.  Last read position: chr1:230,227,613
INFO	2016-11-13 23:41:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:41:30	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:   15s.  Last read position: chr3:37,971,019
INFO	2016-11-13 23:41:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:41:38	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    7s.  Last read position: chr4:176,083,301
INFO	2016-11-13 23:41:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:41:42	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    3s.  Last read position: chr6:19,271,906
INFO	2016-11-13 23:41:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:41:52	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:   10s.  Last read position: chr7:103,399,409
INFO	2016-11-13 23:41:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:41:56	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    3s.  Last read position: chr9:127,802,955
INFO	2016-11-13 23:41:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:42:09	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:   13s.  Last read position: chr11:112,439,415
INFO	2016-11-13 23:42:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:42:11	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    2s.  Last read position: chr13:99,692,765
INFO	2016-11-13 23:42:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:42:22	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:   10s.  Last read position: chr17:8,079,361
INFO	2016-11-13 23:42:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:42:26	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    3s.  Last read position: chr20:28,879,981
INFO	2016-11-13 23:42:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:42:39	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:   13s.  Last read position: chrX:128,251,767
INFO	2016-11-13 23:42:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-13 23:42:40	MarkDuplicates	Read 11151504 records. 0 pairs never matched.
INFO	2016-11-13 23:42:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4166295200; totalMemory: 5313658880; maxMemory: 11453595648
INFO	2016-11-13 23:42:45	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-13 23:42:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-13 23:42:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-13 23:42:46	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-13 23:42:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2370087752; totalMemory: 5313658880; maxMemory: 11453595648
INFO	2016-11-13 23:42:49	MarkDuplicates	Marking 6115486 records as duplicates.
INFO	2016-11-13 23:42:49	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-13 23:45:06	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:16s.  Time for last 10,000,000:  136s.  Last read position: chr20:28,879,981
INFO	2016-11-13 23:45:18	MarkDuplicates	Before output close freeMemory: 8286193520; totalMemory: 8366063616; maxMemory: 11453595648
INFO	2016-11-13 23:45:20	MarkDuplicates	After output close freeMemory: 8170849000; totalMemory: 8250720256; maxMemory: 11453595648
[Sun Nov 13 23:45:21 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.49 minutes.
Runtime.totalMemory()=8250720256

Num	8
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_17
Name	dedup_bam_2 rep1
Thread	thread_41
PID	10877

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

Start	2016-11-13 23:45:24
End	2016-11-13 23:49:14
Elapsed	00:03:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_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/SRR1370905_1/out/align/rep1/SRR1370905_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_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/SRR1370905_1/out/qc/rep1/SRR1370905_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--------------------
4677 (process ID) old priority 0, new priority 10

Num	9
ID	task.postalign_bam.bam_to_tag_rep1.line_505.id_18
Name	bam_to_tag rep1
Thread	thread_41
PID	10893

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

Start	2016-11-13 23:49:16
End	2016-11-13 23:50:51
Elapsed	00:01:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_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/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_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--------------------
8020 (process ID) old priority 0, new priority 10

Waiting for 45 seconds.

Num	10
ID	task.postalign_bed.subsample_tag_rep1.line_45.id_19
Name	subsample_tag rep1
Thread	thread_41
PID	10900

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

Start	2016-11-13 23:50:53
End	2016-11-13 23:52:07
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_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/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_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--------------------
8575 (process ID) old priority 0, new priority 10
Waiting for 50 seconds.

Num	11
ID	task.postalign_bed.spr_rep1.line_255.id_20
Name	spr rep1
Thread	thread_41
PID	10908

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

Start	2016-11-13 23:52:11
End	2016-11-13 23:53:36
Elapsed	00:01:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr2/SRR1370905_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/SRR1370905_1/out/align/rep1/SRR1370905_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/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/pseudo_reps/rep1/pr1/SRR1370905_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--------------------
10388 (process ID) old priority 0, new priority 10
Waiting for 38 seconds.

Num	12
ID	task.postalign_bed.xcor_rep1.line_212.id_21
Name	xcor rep1
Thread	thread_41
PID	10915

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

Start	2016-11-13 23:53:38
End	2016-11-14 00:00:47
Elapsed	00:07:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.plot.pdf
Dependencies

 
# SYS command. line 214

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

# SYS command. line 217

 if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 223

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.15M.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.qc

# SYS command. line 229

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

   
--------------------Stdout--------------------
10680 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.15M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.nodup.15M.tagAlign.gz 
opened /tmp/10915.1.q/Rtmp52zGPG/SRR1370905_1.nodup.15M.tagAlign2a143af47113
done. read 5028949 fragments
ChIP data read length 69 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.06649274 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.114071001291483 
Top 3 estimates for fragment length 160 
Window half size 185 
Phantom peak location 70 
Phantom peak Correlation 0.07000131 
Normalized Strand cross-correlation coefficient (NSC) 1.715541 
Relative Strand cross-correlation Coefficient (RSC) 13.56056 
Phantom Peak Quality Tag 2 
null device 
          1 

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

Num	13
ID	task.postalign_bam.bam_to_tag_ctl1.line_505.id_22
Name	bam_to_tag ctl1
Thread	thread_42
PID	11033

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

Start	2016-11-14 02:08:06
End	2016-11-14 02:14:10
Elapsed	00:06:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_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/SRR1370905_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--------------------
699 (process ID) old priority 0, new priority 10

Num	14
ID	task.graphviz.report.line_97.id_23
Name	report
Thread	thread_Root
PID	1359

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

Start	2016-11-14 02:14:11
End	2016-11-14 02:14:20
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/SRR1370905_1/out/report/SRR1370905_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/report/SRR1370905_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/report/SRR1370905_1_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
1363 (process ID) old priority 0, new priority 10

Num	15
ID	task.report.pdf2png.line_324.id_28
Name	pdf2png
Thread	thread_Root
PID	1398

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

Start	2016-11-14 02:14:12
End	2016-11-14 02:14:21
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_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/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/rep1/SRR1370905_1.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
1402 (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, SRR1370905_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_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	/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:/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:/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:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5:/users/imk1/perl5:/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/SRR1370905_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/SRR1370905_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	14393.SRR1370905_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

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Global scope