Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161110_171001_146
Start time	2016-11-10 17:10:01
Run time	06:27:25.457
Tasks executed	14
Tasks failed	0
Tasks failed names
Arguments*	[-title, SRR1370884_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20161110_171001_146/task.graphviz.report.line_97.id_22 chipseq.bds.20161110_171001_146/task.report.pdf2png.line_324.id_27
thread_41	thread_Root	chipseq.bds.20161110_171001_146_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11 chipseq.bds.20161110_171001_146_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_13 chipseq.bds.20161110_171001_146_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_14 chipseq.bds.20161110_171001_146_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_16 chipseq.bds.20161110_171001_146_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_17 chipseq.bds.20161110_171001_146_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_18 chipseq.bds.20161110_171001_146_parallel_41/task.postalign_bed.spr_rep1.line_255.id_19 chipseq.bds.20161110_171001_146_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_20
thread_42	thread_Root	chipseq.bds.20161110_171001_146_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161110_171001_146_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 chipseq.bds.20161110_171001_146_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20161110_171001_146_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_21

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	6891

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

Start	2016-11-10 17:10:02
End	2016-11-10 17:28:18
Elapsed	00:18:15
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/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_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--------------------
30452 (process ID) old priority 0, new priority 10

Num	2
ID	task.align_bwa.bwa_sam_rep1.line_140.id_11
Name	bwa_sam rep1
Thread	thread_41
PID	6892

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

Start	2016-11-10 17:10:04
End	2016-11-10 17:54:28
Elapsed	00:44:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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--------------------
11025 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.24 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.94 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.15 sec
[bwa_aln_core] refine gapped alignments... 0.74 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.67 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.94 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.58 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.44 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.79 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 1.08 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.35 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.23 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.82 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.79 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.05 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.03 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.76 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.82 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.86 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.51 sec
[bwa_aln_core] refine gapped alignments... 1.35 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.62 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 1.35 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.93 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.48 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.30 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.25 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.60 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.02 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 1.01 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.47 sec
[bwa_aln_core] refine gapped alignments... 1.78 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.60 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.59 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.62 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.97 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.76 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.45 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.31 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.96 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.00 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.48 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.08 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.43 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.50 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.54 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.86 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.12 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.35 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.17 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.30 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.46 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.08 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.84 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 1.10 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.55 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.22 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.91 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.62 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.82 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.85 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 1.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.21 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.18 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.04 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.98 sec
[bwa_aln_core] refine gapped alignments... 0.83 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.26 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.24 sec
[bwa_aln_core] refine gapped alignments... 1.19 sec
[bwa_aln_core] print alignments... 1.24 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.40 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.08 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.71 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.87 sec
[bwa_aln_core] refine gapped alignments... 1.46 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.70 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.21 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.84 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 1.31 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.13 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.22 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.58 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.69 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.63 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.75 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.27 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.29 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.38 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.72 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.69 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.80 sec
[bwa_aln_core] refine gapped alignments... 2.37 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.22 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 1.91 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.31 sec
[bwa_aln_core] refine gapped alignments... 2.20 sec
[bwa_aln_core] print alignments... 1.35 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.43 sec
[bwa_aln_core] refine gapped alignments... 2.81 sec
[bwa_aln_core] print alignments... 1.24 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.85 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.41 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.10 sec
[bwa_aln_core] refine gapped alignments... 2.82 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.09 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.23 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 1.28 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.51 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.84 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 1.25 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.16 sec
[bwa_aln_core] refine gapped alignments... 2.72 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 2.86 sec
[bwa_aln_core] print alignments... 1.27 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.92 sec
[bwa_aln_core] refine gapped alignments... 2.72 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.65 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.57 sec
[bwa_aln_core] refine gapped alignments... 2.74 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.71 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.83 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 1.24 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.30 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 1.09 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.92 sec
[bwa_aln_core] refine gapped alignments... 2.86 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.84 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... 1.12 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.37 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 1.00 sec
[bwa_aln_core] 24076431 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/SRR1370884_1/out/align/rep1/SRR1370884_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_1.fastq.gz
[main] Real time: 1693.679 sec; CPU: 1403.664 sec

Num	3
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	7151

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

Start	2016-11-10 17:28:20
End	2016-11-10 20:42:58
Elapsed	03:14:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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--------------------
20533 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 19:45:19 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Nov 10 19:45:19 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	2016-11-10 19:45:19	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 19:45:19	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 19:45:19	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 19:45:28	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    8s.  Last read position: chr1:22,298,551
INFO	2016-11-10 19:45:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:45:34	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    6s.  Last read position: chr1:41,895,424
INFO	2016-11-10 19:45:34	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:45:41	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    7s.  Last read position: chr1:63,396,527
INFO	2016-11-10 19:45:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:45:55	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:   13s.  Last read position: chr1:89,147,707
INFO	2016-11-10 19:45:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:46:09	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:   14s.  Last read position: chr1:115,615,553
INFO	2016-11-10 19:46:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:46:29	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:   19s.  Last read position: chr1:164,468,682
INFO	2016-11-10 19:46:29	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:46:42	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   13s.  Last read position: chr1:189,102,252
INFO	2016-11-10 19:46:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:46:49	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    7s.  Last read position: chr1:213,979,760
INFO	2016-11-10 19:46:49	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:47:09	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:   19s.  Last read position: chr1:231,814,268
INFO	2016-11-10 19:47:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:47:21	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:   12s.  Last read position: chr2:3,652,468
INFO	2016-11-10 19:47:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:47:40	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:   19s.  Last read position: chr2:39,505,122
INFO	2016-11-10 19:47:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:47:51	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:   10s.  Last read position: chr2:73,561,393
INFO	2016-11-10 19:47:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:48:07	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:   16s.  Last read position: chr2:120,526,571
INFO	2016-11-10 19:48:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:48:21	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:   13s.  Last read position: chr2:160,316,783
INFO	2016-11-10 19:48:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:48:34	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:   13s.  Last read position: chr2:195,549,735
INFO	2016-11-10 19:48:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:48:40	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    5s.  Last read position: chr2:230,358,034
INFO	2016-11-10 19:48:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:48:58	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:   17s.  Last read position: chr3:16,305,780
INFO	2016-11-10 19:48:58	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:49:15	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:   17s.  Last read position: chr3:49,251,279
INFO	2016-11-10 19:49:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:23	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    7s.  Last read position: chr3:84,621,225
INFO	2016-11-10 19:49:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:33	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    9s.  Last read position: chr3:128,121,129
INFO	2016-11-10 19:49:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:39	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    5s.  Last read position: chr3:165,373,238
INFO	2016-11-10 19:49:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:57	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:   18s.  Last read position: chr3:195,333,247
INFO	2016-11-10 19:49:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:04	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:    7s.  Last read position: chr4:37,752,582
INFO	2016-11-10 19:50:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:14	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    9s.  Last read position: chr4:81,286,306
INFO	2016-11-10 19:50:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:21	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    7s.  Last read position: chr4:119,339,736
INFO	2016-11-10 19:50:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:32	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:   10s.  Last read position: chr4:158,818,783
INFO	2016-11-10 19:50:32	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:50:52	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:   19s.  Last read position: chr5:6,447,551
INFO	2016-11-10 19:50:52	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 19:51:00	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:05:40s.  Time for last 1,000,000:    8s.  Last read position: chr5:33,219,021
INFO	2016-11-10 19:51:00	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:51:06	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    5s.  Last read position: chr5:60,694,078
INFO	2016-11-10 19:51:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:51:17	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:   10s.  Last read position: chr5:86,336,676
INFO	2016-11-10 19:51:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:28	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:   11s.  Last read position: chr5:112,930,184
INFO	2016-11-10 19:51:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:51:47	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:   18s.  Last read position: chr5:136,852,889
INFO	2016-11-10 19:51:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:54	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    6s.  Last read position: chr5:160,271,193
INFO	2016-11-10 19:51:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:01	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    7s.  Last read position: chr6:4,126,386
INFO	2016-11-10 19:52:01	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:52:10	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    9s.  Last read position: chr6:28,666,579
INFO	2016-11-10 19:52:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:20	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:   10s.  Last read position: chr6:49,527,281
INFO	2016-11-10 19:52:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:27	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    7s.  Last read position: chr6:81,728,195
INFO	2016-11-10 19:52:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:47	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:   20s.  Last read position: chr6:107,535,760
INFO	2016-11-10 19:52:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:55	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    7s.  Last read position: chr6:132,364,408
INFO	2016-11-10 19:52:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:53:03	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    8s.  Last read position: chr6:156,918,595
INFO	2016-11-10 19:53:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:09	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:07:49s.  Time for last 1,000,000:    5s.  Last read position: chr7:18,636,743
INFO	2016-11-10 19:53:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:18	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    9s.  Last read position: chr7:53,850,313
INFO	2016-11-10 19:53:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:36	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:   17s.  Last read position: chr7:96,503,433
INFO	2016-11-10 19:53:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:41	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:08:21s.  Time for last 1,000,000:    5s.  Last read position: chr7:120,651,846
INFO	2016-11-10 19:53:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:29	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:   47s.  Last read position: chr7:146,401,497
INFO	2016-11-10 19:54:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:36	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:09:16s.  Time for last 1,000,000:    6s.  Last read position: chr8:17,030,519
INFO	2016-11-10 19:54:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:44	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    8s.  Last read position: chr8:42,750,671
INFO	2016-11-10 19:54:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:50	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:09:30s.  Time for last 1,000,000:    6s.  Last read position: chr8:85,385,487
INFO	2016-11-10 19:54:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:01	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:   10s.  Last read position: chr8:124,358,985
INFO	2016-11-10 19:55:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:14	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:09:54s.  Time for last 1,000,000:   12s.  Last read position: chr9:18,183,883
INFO	2016-11-10 19:55:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:20	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:10:00s.  Time for last 1,000,000:    6s.  Last read position: chr9:84,163,983
INFO	2016-11-10 19:55:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:26	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    5s.  Last read position: chr9:119,875,535
INFO	2016-11-10 19:55:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:31	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:    5s.  Last read position: chr10:5,661,683
INFO	2016-11-10 19:55:31	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:55:37	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    5s.  Last read position: chr10:29,748,948
INFO	2016-11-10 19:55:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:43	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:10:23s.  Time for last 1,000,000:    5s.  Last read position: chr10:61,280,221
INFO	2016-11-10 19:55:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:53	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:10:33s.  Time for last 1,000,000:    9s.  Last read position: chr10:85,305,552
INFO	2016-11-10 19:55:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:56:06	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:10:46s.  Time for last 1,000,000:   13s.  Last read position: chr10:108,129,202
INFO	2016-11-10 19:56:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:12	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:10:52s.  Time for last 1,000,000:    5s.  Last read position: chr10:132,730,123
INFO	2016-11-10 19:56:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:17	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:10:57s.  Time for last 1,000,000:    4s.  Last read position: chr11:35,359,267
INFO	2016-11-10 19:56:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:27	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:11:07s.  Time for last 1,000,000:    9s.  Last read position: chr11:75,696,431
INFO	2016-11-10 19:56:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:38	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:   11s.  Last read position: chr11:114,414,621
INFO	2016-11-10 19:56:38	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:56:44	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:11:24s.  Time for last 1,000,000:    5s.  Last read position: chr12:8,900,276
INFO	2016-11-10 19:56:44	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:56:53	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:11:33s.  Time for last 1,000,000:    9s.  Last read position: chr12:38,863,889
INFO	2016-11-10 19:56:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:14	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:11:54s.  Time for last 1,000,000:   20s.  Last read position: chr12:60,598,824
INFO	2016-11-10 19:57:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:19	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:11:59s.  Time for last 1,000,000:    5s.  Last read position: chr12:88,520,538
INFO	2016-11-10 19:57:19	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:57:25	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:12:05s.  Time for last 1,000,000:    5s.  Last read position: chr12:112,268,437
INFO	2016-11-10 19:57:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:33	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:12:13s.  Time for last 1,000,000:    8s.  Last read position: chr13:23,999,632
INFO	2016-11-10 19:57:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:43	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:12:23s.  Time for last 1,000,000:    9s.  Last read position: chr13:51,165,870
INFO	2016-11-10 19:57:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:57:51	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:12:31s.  Time for last 1,000,000:    8s.  Last read position: chr13:88,986,369
INFO	2016-11-10 19:57:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:58	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:12:38s.  Time for last 1,000,000:    6s.  Last read position: chr14:23,149,367
INFO	2016-11-10 19:57:58	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:15	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:   17s.  Last read position: chr14:58,140,905
INFO	2016-11-10 19:58:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:27	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:13:07s.  Time for last 1,000,000:   11s.  Last read position: chr14:91,912,553
INFO	2016-11-10 19:58:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:58:39	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:13:19s.  Time for last 1,000,000:   12s.  Last read position: chr15:38,895,095
INFO	2016-11-10 19:58:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:45	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:13:25s.  Time for last 1,000,000:    5s.  Last read position: chr15:68,188,367
INFO	2016-11-10 19:58:45	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:52	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:13:32s.  Time for last 1,000,000:    7s.  Last read position: chr15:87,921,272
INFO	2016-11-10 19:58:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:03	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:13:43s.  Time for last 1,000,000:   11s.  Last read position: chr16:11,143,813
INFO	2016-11-10 19:59:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:10	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:13:50s.  Time for last 1,000,000:    6s.  Last read position: chr16:51,391,437
INFO	2016-11-10 19:59:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:59:17	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:13:57s.  Time for last 1,000,000:    6s.  Last read position: chr16:84,928,458
INFO	2016-11-10 19:59:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:36	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:14:16s.  Time for last 1,000,000:   19s.  Last read position: chr17:18,368,935
INFO	2016-11-10 19:59:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:45	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:14:25s.  Time for last 1,000,000:    8s.  Last read position: chr17:44,246,522
INFO	2016-11-10 19:59:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:52	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:14:32s.  Time for last 1,000,000:    7s.  Last read position: chr17:66,172,158
INFO	2016-11-10 19:59:52	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 20:00:01	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:14:41s.  Time for last 1,000,000:    8s.  Last read position: chr18:5,619,614
INFO	2016-11-10 20:00:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:00:11	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:14:51s.  Time for last 1,000,000:   10s.  Last read position: chr18:46,152,631
INFO	2016-11-10 20:00:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:00:18	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:14:58s.  Time for last 1,000,000:    7s.  Last read position: chr19:1,328,731
INFO	2016-11-10 20:00:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:00:27	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:15:07s.  Time for last 1,000,000:    8s.  Last read position: chr19:28,148,444
INFO	2016-11-10 20:00:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:00:37	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:15:17s.  Time for last 1,000,000:   10s.  Last read position: chr19:40,341,579
INFO	2016-11-10 20:00:37	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:00:57	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:15:37s.  Time for last 1,000,000:   19s.  Last read position: chr20:3,222,035
INFO	2016-11-10 20:00:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:07	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:15:47s.  Time for last 1,000,000:   10s.  Last read position: chr20:37,218,903
INFO	2016-11-10 20:01:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:53	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:16:33s.  Time for last 1,000,000:   45s.  Last read position: chr20:62,871,367
INFO	2016-11-10 20:01:53	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 20:01:59	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:16:39s.  Time for last 1,000,000:    6s.  Last read position: chr21:39,474,524
INFO	2016-11-10 20:01:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:02:09	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:16:49s.  Time for last 1,000,000:    9s.  Last read position: chr22:31,346,944
INFO	2016-11-10 20:02:09	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:02:14	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:16:54s.  Time for last 1,000,000:    5s.  Last read position: chrX:6,235,951
INFO	2016-11-10 20:02:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:02:24	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:17:04s.  Time for last 1,000,000:   10s.  Last read position: chrX:38,820,975
INFO	2016-11-10 20:02:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:02:33	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:17:13s.  Time for last 1,000,000:    8s.  Last read position: chrX:69,473,954
INFO	2016-11-10 20:02:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:02:40	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:17:20s.  Time for last 1,000,000:    7s.  Last read position: chrX:92,683,143
INFO	2016-11-10 20:02:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:02:45	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:17:25s.  Time for last 1,000,000:    4s.  Last read position: chrX:118,447,518
INFO	2016-11-10 20:02:45	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:03:02	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:17:42s.  Time for last 1,000,000:   16s.  Last read position: chrX:142,819,613
INFO	2016-11-10 20:03:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:03:08	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:17:48s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,995
INFO	2016-11-10 20:03:08	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 20:03:13	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:17:53s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,775
INFO	2016-11-10 20:03:13	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 20:03:19	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 20:03:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 5971446568; totalMemory: 6050807808; maxMemory: 11453595648
INFO	2016-11-10 20:03:26	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 20:03:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 20:03:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 20:04:14	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 20:04:15	MarkDuplicates	After generateDuplicateIndexes freeMemory: 6097247152; totalMemory: 9038725120; maxMemory: 11453595648
INFO	2016-11-10 20:04:15	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 20:04:15	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-10 20:07:10	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:54s.  Time for last 10,000,000:  174s.  Last read position: chr2:3,652,468
INFO	2016-11-10 20:10:06	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:05:50s.  Time for last 10,000,000:  176s.  Last read position: chr3:128,121,129
INFO	2016-11-10 20:13:27	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:09:12s.  Time for last 10,000,000:  201s.  Last read position: chr5:86,336,676
INFO	2016-11-10 20:16:32	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:12:16s.  Time for last 10,000,000:  184s.  Last read position: chr6:156,918,595
INFO	2016-11-10 20:19:34	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:15:18s.  Time for last 10,000,000:  181s.  Last read position: chr9:18,183,883
INFO	2016-11-10 20:22:55	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:18:40s.  Time for last 10,000,000:  201s.  Last read position: chr11:75,696,431
INFO	2016-11-10 20:27:07	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:22:52s.  Time for last 10,000,000:  251s.  Last read position: chr14:23,149,367
INFO	2016-11-10 20:32:26	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:28:10s.  Time for last 10,000,000:  318s.  Last read position: chr17:44,246,522
INFO	2016-11-10 20:39:28	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:35:13s.  Time for last 10,000,000:  422s.  Last read position: chr21:39,474,524
INFO	2016-11-10 20:42:47	MarkDuplicates	Before output close freeMemory: 9029362384; totalMemory: 9114222592; maxMemory: 11453595648
INFO	2016-11-10 20:42:52	MarkDuplicates	After output close freeMemory: 9026739888; totalMemory: 9111601152; maxMemory: 11453595648
[Thu Nov 10 20:42:57 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 57.63 minutes.
Runtime.totalMemory()=9111601152

Num	4
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_13
Name	dedup_bam_1 rep1
Thread	thread_41
PID	7178

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

Start	2016-11-10 17:54:31
End	2016-11-10 20:37:25
Elapsed	02:42:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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--------------------
19563 (process ID) old priority 0, new priority 10

Num	5
ID	task.postalign_bam.markdup_bam_picard_rep1.line_348.id_14
Name	markdup_bam_picard rep1
Thread	thread_41
PID	7368

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

Start	2016-11-10 20:37:27
End	2016-11-10 21:38:20
Elapsed	01:00:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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--------------------
34857 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 21:32:52 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Nov 10 21:32:52 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-10 21:32:52	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 21:32:52	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 21:32:52	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 21:33:06	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:   12s.  Last read position: chr1:119,713,213
INFO	2016-11-10 21:33:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:33:18	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:   11s.  Last read position: chr2:23,942,929
INFO	2016-11-10 21:33:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:33:24	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    6s.  Last read position: chr2:216,559,176
INFO	2016-11-10 21:33:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:33:30	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    6s.  Last read position: chr3:149,197,227
INFO	2016-11-10 21:33:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:33:39	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    8s.  Last read position: chr4:138,186,595
INFO	2016-11-10 21:33:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:33:45	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    6s.  Last read position: chr5:96,392,763
INFO	2016-11-10 21:33:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:33:50	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    5s.  Last read position: chr6:39,624,633
INFO	2016-11-10 21:33:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:33:58	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    7s.  Last read position: chr7:10,554,712
INFO	2016-11-10 21:33:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:06	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    8s.  Last read position: chr8:17,064,069
INFO	2016-11-10 21:34:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:15	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    8s.  Last read position: chr9:79,965,829
INFO	2016-11-10 21:34:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:21	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    6s.  Last read position: chr10:86,079,346
INFO	2016-11-10 21:34:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:25	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    4s.  Last read position: chr11:118,529,371
INFO	2016-11-10 21:34:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:32	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    6s.  Last read position: chr12:116,771,051
INFO	2016-11-10 21:34:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:39	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    7s.  Last read position: chr14:57,595,162
INFO	2016-11-10 21:34:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:42	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    3s.  Last read position: chr16:24,862,009
INFO	2016-11-10 21:34:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:51	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    8s.  Last read position: chr18:9,512,344
INFO	2016-11-10 21:34:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:34:54	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    3s.  Last read position: chr20:19,392,476
INFO	2016-11-10 21:34:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:35:01	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    6s.  Last read position: chrX:24,254,504
INFO	2016-11-10 21:35:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:35:05	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    4s.  Last read position: chrM:439
INFO	2016-11-10 21:35:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:35:05	MarkDuplicates	Read 19051583 records. 0 pairs never matched.
INFO	2016-11-10 21:35:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4073167864; totalMemory: 5725224960; maxMemory: 11453595648
INFO	2016-11-10 21:35:10	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 21:35:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 21:35:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 21:35:12	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 21:35:13	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2783485840; totalMemory: 5725224960; maxMemory: 11453595648
INFO	2016-11-10 21:35:13	MarkDuplicates	Marking 4619314 records as duplicates.
INFO	2016-11-10 21:35:13	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-10 21:36:52	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:38s.  Time for last 10,000,000:   98s.  Last read position: chr9:79,965,829
INFO	2016-11-10 21:38:18	MarkDuplicates	Before output close freeMemory: 8379893392; totalMemory: 8461484032; maxMemory: 11453595648
INFO	2016-11-10 21:38:18	MarkDuplicates	After output close freeMemory: 8497815472; totalMemory: 8579448832; maxMemory: 11453595648
[Thu Nov 10 21:38:18 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 5.43 minutes.
Runtime.totalMemory()=8579448832

Num	6
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	7375

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

Start	2016-11-10 20:42:59
End	2016-11-10 23:28:17
Elapsed	02:45:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_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/SRR1370884_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--------------------
56075 (process ID) old priority 0, new priority 10

Num	7
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_16
Name	dedup_bam_2 rep1
Thread	thread_41
PID	7492

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

Start	2016-11-10 21:38:22
End	2016-11-10 21:55:54
Elapsed	00:17:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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/SRR1370884_1/out/qc/rep1/SRR1370884_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--------------------
8454 (process ID) old priority 0, new priority 10

Num	8
ID	task.postalign_bam.bam_to_tag_rep1.line_505.id_17
Name	bam_to_tag rep1
Thread	thread_41
PID	7567

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

Start	2016-11-10 21:55:55
End	2016-11-10 22:04:14
Elapsed	00:08:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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--------------------
36068 (process ID) old priority 0, new priority 10

Num	9
ID	task.postalign_bed.subsample_tag_rep1.line_45.id_18
Name	subsample_tag rep1
Thread	thread_41
PID	7614

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

Start	2016-11-10 22:04:17
End	2016-11-10 22:07:07
Elapsed	00:02:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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--------------------
10787 (process ID) old priority 0, new priority 10
Waiting for 29 seconds.

Num	10
ID	task.postalign_bed.spr_rep1.line_255.id_19
Name	spr rep1
Thread	thread_41
PID	7644

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

Start	2016-11-10 22:07:09
End	2016-11-10 22:12:27
Elapsed	00:05:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/pseudo_reps/rep1/pr1/SRR1370884_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--------------------
12650 (process ID) old priority 0, new priority 10

Num	11
ID	task.postalign_bed.xcor_rep1.line_212.id_20
Name	xcor rep1
Thread	thread_41
PID	7681

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

Start	2016-11-10 22:12:28
End	2016-11-10 22:35:08
Elapsed	00:22:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.15M.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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--------------------
16965 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_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/SRR1370884_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/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.nodup.15M.tagAlign.gz 
opened /tmp/7681.1.q/RtmpS0evhh/SRR1370884_1.nodup.15M.tagAlign43151eb3f845
done. read 14418937 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1684911 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.196412893906975 
Top 3 estimates for fragment length 150 
Window half size 175 
Phantom peak location 55 
Phantom peak Correlation 0.1739064 
Normalized Strand cross-correlation coefficient (NSC) 1.165717 
Relative Strand cross-correlation Coefficient (RSC) 5.156098 
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	12
ID	task.postalign_bam.bam_to_tag_ctl1.line_505.id_21
Name	bam_to_tag ctl1
Thread	thread_42
PID	7903

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

Start	2016-11-10 23:28:21
End	2016-11-10 23:37:10
Elapsed	00:08:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_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/SRR1370884_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--------------------
26764 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_22
Name	report
Thread	thread_Root
PID	33338

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

Start	2016-11-10 23:37:11
End	2016-11-10 23:37:25
Elapsed	00:00:14
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/SRR1370884_1/out/report/SRR1370884_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/report/SRR1370884_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/report/SRR1370884_1_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
33342 (process ID) old priority 0, new priority 10

Num	14
ID	task.report.pdf2png.line_324.id_27
Name	pdf2png
Thread	thread_Root
PID	33394

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

Start	2016-11-10 23:37:11
End	2016-11-10 23:37:26
Elapsed	00:00:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_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/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
33399 (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, SRR1370884_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $]
string	ASCPKEY	/software/ascp/etc/asperaweb_id_dsa.openssh
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_N5SeQf
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_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	29642.SRR1370884_1.BDS
string	system	sge
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int	timeout	-1
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	20
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope