Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161110_171005_025
Start time	2016-11-10 17:10:05
Run time	2 days 19:56:30.018
Tasks executed	6
Tasks failed	2
Tasks failed names	dedup_bam_2 ctl1 markdup_bam_picard rep1
Arguments*	[-title, SRR1370886_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370886_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
thread_42	thread_Root	chipseq.bds.20161110_171005_025_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161110_171005_025_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 chipseq.bds.20161110_171005_025_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
thread_41	thread_Root	chipseq.bds.20161110_171005_025_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11 chipseq.bds.20161110_171005_025_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_13 chipseq.bds.20161110_171005_025_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_14

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	6895

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

Start	2016-11-10 17:10:07
End	2016-11-10 17:28:53
Elapsed	00:18:45
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/SRR1370886_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/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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/SRR1370886_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--------------------
30453 (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	6896

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

Start	2016-11-10 17:10:07
End	2016-11-10 17:55:21
Elapsed	00:45:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370886_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_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/SRR1370886_1/out/align/rep1/SRR1370886_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370886_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_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--------------------
11027 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.54 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.90 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.92 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.96 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.82 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.93 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.93 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.07 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.34 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.55 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.66 sec
[bwa_aln_core] refine gapped alignments... 1.07 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.04 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.66 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.22 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.17 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.03 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.97 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.11 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.73 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.74 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.01 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.95 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.60 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.64 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.02 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.08 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.02 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.79 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.52 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.12 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.23 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 1.01 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.90 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.79 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.70 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.99 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.59 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.75 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.11 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.97 sec
[bwa_aln_core] refine gapped alignments... 1.08 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.56 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.59 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.31 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.87 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.00 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.72 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.62 sec
[bwa_aln_core] refine gapped alignments... 1.07 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.42 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.71 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.05 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.45 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.46 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.50 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.04 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.44 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.18 sec
[bwa_aln_core] refine gapped alignments... 1.09 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.29 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 1.09 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.85 sec
[bwa_aln_core] refine gapped alignments... 2.16 sec
[bwa_aln_core] print alignments... 1.09 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.94 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.33 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.29 sec
[bwa_aln_core] refine gapped alignments... 1.12 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.79 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.75 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.49 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.37 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.94 sec
[bwa_aln_core] refine gapped alignments... 1.14 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.21 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.48 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.82 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.88 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.50 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.22 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.89 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 1.12 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.69 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.47 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 1.28 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.66 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.54 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.57 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.99 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.20 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.88 sec
[bwa_aln_core] refine gapped alignments... 1.09 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.92 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.26 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 0.96 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.84 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.34 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.17 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.71 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.61 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.24 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.96 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.69 sec
[bwa_aln_core] refine gapped alignments... 1.43 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.94 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.42 sec
[bwa_aln_core] refine gapped alignments... 1.32 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.10 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.25 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.27 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.23 sec
[bwa_aln_core] refine gapped alignments... 1.64 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.67 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.65 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.01 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.99 sec
[bwa_aln_core] refine gapped alignments... 1.15 sec
[bwa_aln_core] print alignments... 1.30 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.38 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.43 sec
[bwa_aln_core] refine gapped alignments... 2.89 sec
[bwa_aln_core] print alignments... 1.35 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.81 sec
[bwa_aln_core] refine gapped alignments... 2.84 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.60 sec
[bwa_aln_core] refine gapped alignments... 2.83 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.29 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.03 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 1.28 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.55 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 1.06 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.54 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 1.08 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.28 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.77 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.08 sec
[bwa_aln_core] 25971025 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/SRR1370886_1/out/align/rep1/SRR1370886_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370886_1.fastq.gz
[main] Real time: 1604.396 sec; CPU: 1312.312 sec

Num	3
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	7153

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

Start	2016-11-10 17:28:55
End	2016-11-10 20:56:28
Elapsed	03:27:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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--------------------
46864 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 19:47:49 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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 19:47:49 PST 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-10 19:47:50	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 19:47:50	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 19:47:50	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 19:47:58	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr1:22,298,551
INFO	2016-11-10 19:47:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:48:04	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    5s.  Last read position: chr1:41,895,424
INFO	2016-11-10 19:48:04	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:48:09	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    5s.  Last read position: chr1:63,396,527
INFO	2016-11-10 19:48:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:48:16	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    6s.  Last read position: chr1:89,147,707
INFO	2016-11-10 19:48:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:48:25	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    8s.  Last read position: chr1:115,615,553
INFO	2016-11-10 19:48:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:48:30	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    4s.  Last read position: chr1:164,468,682
INFO	2016-11-10 19:48:30	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:48:37	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    7s.  Last read position: chr1:189,102,252
INFO	2016-11-10 19:48:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:48:43	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    5s.  Last read position: chr1:213,979,760
INFO	2016-11-10 19:48:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:48:48	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    4s.  Last read position: chr1:231,814,268
INFO	2016-11-10 19:48:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:48:54	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    6s.  Last read position: chr2:3,652,468
INFO	2016-11-10 19:48:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:49:02	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    7s.  Last read position: chr2:39,505,122
INFO	2016-11-10 19:49:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:09	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:18s.  Time for last 1,000,000:    6s.  Last read position: chr2:73,561,393
INFO	2016-11-10 19:49:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:49:14	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    5s.  Last read position: chr2:120,526,571
INFO	2016-11-10 19:49:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:22	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    7s.  Last read position: chr2:160,316,783
INFO	2016-11-10 19:49:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:31	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    9s.  Last read position: chr2:195,549,735
INFO	2016-11-10 19:49:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:49:38	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    6s.  Last read position: chr2:230,358,034
INFO	2016-11-10 19:49:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:49:44	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    6s.  Last read position: chr3:16,305,780
INFO	2016-11-10 19:49:44	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:49:48	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    4s.  Last read position: chr3:49,251,279
INFO	2016-11-10 19:49:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:49:55	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    6s.  Last read position: chr3:84,621,225
INFO	2016-11-10 19:49:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:05	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:   10s.  Last read position: chr3:128,121,129
INFO	2016-11-10 19:50:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:10	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    4s.  Last read position: chr3:165,373,238
INFO	2016-11-10 19:50:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:15	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    5s.  Last read position: chr3:195,333,247
INFO	2016-11-10 19:50:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:21	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    5s.  Last read position: chr4:37,752,582
INFO	2016-11-10 19:50:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:50:26	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    5s.  Last read position: chr4:81,286,306
INFO	2016-11-10 19:50:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:31	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    4s.  Last read position: chr4:119,339,736
INFO	2016-11-10 19:50:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:50:41	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:   10s.  Last read position: chr4:158,818,783
INFO	2016-11-10 19:50:41	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:50:46	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    4s.  Last read position: chr5:6,447,551
INFO	2016-11-10 19:50:46	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 19:50:51	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    5s.  Last read position: chr5:33,219,021
INFO	2016-11-10 19:50:51	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:50:55	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    4s.  Last read position: chr5:60,694,078
INFO	2016-11-10 19:50:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:51:01	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    5s.  Last read position: chr5:86,336,676
INFO	2016-11-10 19:51:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:11	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    9s.  Last read position: chr5:112,930,184
INFO	2016-11-10 19:51:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:51:14	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    3s.  Last read position: chr5:136,852,889
INFO	2016-11-10 19:51:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:19	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    4s.  Last read position: chr5:160,271,193
INFO	2016-11-10 19:51:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:24	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    4s.  Last read position: chr6:4,126,386
INFO	2016-11-10 19:51:24	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:51:32	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    7s.  Last read position: chr6:28,666,579
INFO	2016-11-10 19:51:32	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:35	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    3s.  Last read position: chr6:49,527,281
INFO	2016-11-10 19:51:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:41	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    5s.  Last read position: chr6:81,728,195
INFO	2016-11-10 19:51:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:54	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:   13s.  Last read position: chr6:107,535,760
INFO	2016-11-10 19:51:54	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:51:59	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    4s.  Last read position: chr6:132,364,408
INFO	2016-11-10 19:51:59	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:52:03	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    4s.  Last read position: chr6:156,918,595
INFO	2016-11-10 19:52:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:09	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    5s.  Last read position: chr7:18,636,743
INFO	2016-11-10 19:52:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:14	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    5s.  Last read position: chr7:53,850,313
INFO	2016-11-10 19:52:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:52:18	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    3s.  Last read position: chr7:96,503,433
INFO	2016-11-10 19:52:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:26	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    7s.  Last read position: chr7:120,651,846
INFO	2016-11-10 19:52:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:06	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:   40s.  Last read position: chr7:146,401,497
INFO	2016-11-10 19:53:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:14	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    8s.  Last read position: chr8:17,030,519
INFO	2016-11-10 19:53:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:18	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    4s.  Last read position: chr8:42,750,671
INFO	2016-11-10 19:53:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:23	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    4s.  Last read position: chr8:85,385,487
INFO	2016-11-10 19:53:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:27	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    4s.  Last read position: chr8:124,358,985
INFO	2016-11-10 19:53:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:32	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    4s.  Last read position: chr9:18,183,883
INFO	2016-11-10 19:53:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:35	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    3s.  Last read position: chr9:84,163,983
INFO	2016-11-10 19:53:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:40	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    4s.  Last read position: chr9:119,875,535
INFO	2016-11-10 19:53:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:49	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    9s.  Last read position: chr10:5,661,683
INFO	2016-11-10 19:53:49	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:53:53	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    3s.  Last read position: chr10:29,748,948
INFO	2016-11-10 19:53:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:58	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    5s.  Last read position: chr10:61,280,221
INFO	2016-11-10 19:53:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:02	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    4s.  Last read position: chr10:85,305,552
INFO	2016-11-10 19:54:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:54:08	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    5s.  Last read position: chr10:108,129,202
INFO	2016-11-10 19:54:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:11	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    3s.  Last read position: chr10:132,730,123
INFO	2016-11-10 19:54:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:17	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    5s.  Last read position: chr11:35,359,267
INFO	2016-11-10 19:54:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:25	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    8s.  Last read position: chr11:75,696,431
INFO	2016-11-10 19:54:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:37	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:   12s.  Last read position: chr11:114,414,621
INFO	2016-11-10 19:54:37	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:54:41	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    3s.  Last read position: chr12:8,900,276
INFO	2016-11-10 19:54:41	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:54:45	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    3s.  Last read position: chr12:38,863,889
INFO	2016-11-10 19:54:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:49	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    4s.  Last read position: chr12:60,598,824
INFO	2016-11-10 19:54:49	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:54	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    4s.  Last read position: chr12:88,520,538
INFO	2016-11-10 19:54:54	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:55:01	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    7s.  Last read position: chr12:112,268,437
INFO	2016-11-10 19:55:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:09	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    7s.  Last read position: chr13:23,999,632
INFO	2016-11-10 19:55:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:15	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    5s.  Last read position: chr13:51,165,870
INFO	2016-11-10 19:55:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:21	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    6s.  Last read position: chr13:88,986,369
INFO	2016-11-10 19:55:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:24	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    3s.  Last read position: chr14:23,149,367
INFO	2016-11-10 19:55:24	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:55:36	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:   11s.  Last read position: chr14:58,140,905
INFO	2016-11-10 19:55:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:41	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    4s.  Last read position: chr14:91,912,553
INFO	2016-11-10 19:55:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:46	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:07:55s.  Time for last 1,000,000:    5s.  Last read position: chr15:38,895,095
INFO	2016-11-10 19:55:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:55	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    9s.  Last read position: chr15:68,188,367
INFO	2016-11-10 19:55:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:56:02	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:08:12s.  Time for last 1,000,000:    7s.  Last read position: chr15:87,921,272
INFO	2016-11-10 19:56:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:08	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    6s.  Last read position: chr16:11,143,813
INFO	2016-11-10 19:56:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:14	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    5s.  Last read position: chr16:51,391,437
INFO	2016-11-10 19:56:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:56:18	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    3s.  Last read position: chr16:84,928,458
INFO	2016-11-10 19:56:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:25	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:08:34s.  Time for last 1,000,000:    7s.  Last read position: chr17:18,368,935
INFO	2016-11-10 19:56:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:40	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:   15s.  Last read position: chr17:44,246,522
INFO	2016-11-10 19:56:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:45	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    4s.  Last read position: chr17:66,172,158
INFO	2016-11-10 19:56:45	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 19:56:49	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    3s.  Last read position: chr18:5,619,614
INFO	2016-11-10 19:56:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:54	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    5s.  Last read position: chr18:46,152,631
INFO	2016-11-10 19:56:54	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:02	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:09:11s.  Time for last 1,000,000:    7s.  Last read position: chr19:1,328,731
INFO	2016-11-10 19:57:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:05	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    3s.  Last read position: chr19:28,148,444
INFO	2016-11-10 19:57:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:11	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    5s.  Last read position: chr19:40,341,579
INFO	2016-11-10 19:57:11	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:57:16	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    5s.  Last read position: chr20:3,222,035
INFO	2016-11-10 19:57:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:21	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    5s.  Last read position: chr20:37,218,903
INFO	2016-11-10 19:57:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:57	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:10:06s.  Time for last 1,000,000:   35s.  Last read position: chr20:62,871,367
INFO	2016-11-10 19:57:57	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 19:58:02	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:10:12s.  Time for last 1,000,000:    5s.  Last read position: chr21:39,474,524
INFO	2016-11-10 19:58:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:07	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:10:16s.  Time for last 1,000,000:    4s.  Last read position: chr22:31,346,944
INFO	2016-11-10 19:58:07	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:12	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:10:22s.  Time for last 1,000,000:    5s.  Last read position: chrX:6,235,951
INFO	2016-11-10 19:58:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:58:22	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:   10s.  Last read position: chrX:38,820,975
INFO	2016-11-10 19:58:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:31	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:    8s.  Last read position: chrX:69,473,954
INFO	2016-11-10 19:58:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:41	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:   10s.  Last read position: chrX:92,683,143
INFO	2016-11-10 19:58:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:45	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:10:55s.  Time for last 1,000,000:    4s.  Last read position: chrX:118,447,518
INFO	2016-11-10 19:58:45	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:58:49	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:10:59s.  Time for last 1,000,000:    3s.  Last read position: chrX:142,819,613
INFO	2016-11-10 19:58:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:59:01	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:11:10s.  Time for last 1,000,000:   11s.  Last read position: chrM:3,995
INFO	2016-11-10 19:59:01	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 19:59:06	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:11:15s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,775
INFO	2016-11-10 19:59:06	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 19:59:10	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 19:59:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 5690207800; totalMemory: 5770313728; maxMemory: 11453595648
INFO	2016-11-10 19:59:17	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 19:59:17	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 19:59:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 19:59:55	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 19:59:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5806090392; totalMemory: 8747745280; maxMemory: 11453595648
INFO	2016-11-10 19:59:56	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 19:59:56	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-10 20:02:53	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:57s.  Time for last 10,000,000:  177s.  Last read position: chr2:3,652,468
INFO	2016-11-10 20:05:48	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:05:52s.  Time for last 10,000,000:  174s.  Last read position: chr3:128,121,129
INFO	2016-11-10 20:08:30	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:08:33s.  Time for last 10,000,000:  161s.  Last read position: chr5:86,336,676
INFO	2016-11-10 20:11:31	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:11:34s.  Time for last 10,000,000:  181s.  Last read position: chr6:156,918,595
INFO	2016-11-10 20:14:51	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:14:54s.  Time for last 10,000,000:  199s.  Last read position: chr9:18,183,883
INFO	2016-11-10 20:20:17	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:20:21s.  Time for last 10,000,000:  326s.  Last read position: chr11:75,696,431
INFO	2016-11-10 20:29:09	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:29:13s.  Time for last 10,000,000:  531s.  Last read position: chr14:23,149,367
INFO	2016-11-10 20:38:08	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:38:12s.  Time for last 10,000,000:  539s.  Last read position: chr17:44,246,522
INFO	2016-11-10 20:47:23	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:47:27s.  Time for last 10,000,000:  555s.  Last read position: chr21:39,474,524
INFO	2016-11-10 20:55:56	MarkDuplicates	Before output close freeMemory: 8754957936; totalMemory: 8840019968; maxMemory: 11453595648
INFO	2016-11-10 20:56:25	MarkDuplicates	After output close freeMemory: 8752335440; totalMemory: 8837398528; maxMemory: 11453595648
[Thu Nov 10 20:56:26 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 68.61 minutes.
Runtime.totalMemory()=8837398528

Num	4
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_13
Name	dedup_bam_1 rep1
Thread	thread_41
PID	7179

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

Start	2016-11-10 17:55:22
End	2016-11-10 20:44:04
Elapsed	02:48:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_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/SRR1370886_1/out/align/rep1/SRR1370886_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_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/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_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--------------------
19561 (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	7379

OK	false
Exit Code	3
Retries
State	RUNNING
Dep.	WAIT
Cpus	1
Mem

Start	2016-11-10 20:44:05
End	2016-11-10 20:44:05
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_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/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_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--------------------
30622 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 21:35:13 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/rep1/SRR1370886_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/rep1/SRR1370886_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 21:35:13 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 21:35:18	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 21:35:18	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 21:35:18	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 21:35:41	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:   17s.  Last read position: chr1:93,083,166
INFO	2016-11-10 21:35:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:35:56	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:   14s.  Last read position: chr1:228,173,842
INFO	2016-11-10 21:35:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:36:11	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:   15s.  Last read position: chr2:144,263,129
INFO	2016-11-10 21:36:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:36:21	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:   10s.  Last read position: chr3:61,247,241
INFO	2016-11-10 21:36:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:36:37	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:   15s.  Last read position: chr4:66,490,141
INFO	2016-11-10 21:36:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:36:49	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:   11s.  Last read position: chr5:68,415,891
INFO	2016-11-10 21:36:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:37:01	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:   12s.  Last read position: chr6:10,415,000
INFO	2016-11-10 21:37:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:37:18	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:   16s.  Last read position: chr6:147,253,177
INFO	2016-11-10 21:37:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:37:37	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:   19s.  Last read position: chr7:137,470,339
INFO	2016-11-10 21:37:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:37:45	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    8s.  Last read position: chr9:5,415,036
INFO	2016-11-10 21:37:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:37:58	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:   12s.  Last read position: chr10:37,297,980
INFO	2016-11-10 21:37:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:38:07	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    9s.  Last read position: chr11:31,770,284
INFO	2016-11-10 21:38:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:38:26	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:   19s.  Last read position: chr12:49,197,507
INFO	2016-11-10 21:38:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:38:36	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    9s.  Last read position: chr13:52,351,689
INFO	2016-11-10 21:38:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:38:57	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:   20s.  Last read position: chr15:41,004,632
INFO	2016-11-10 21:38:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:39:03	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    6s.  Last read position: chr16:58,464,097
INFO	2016-11-10 21:39:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:39:25	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:04:01s.  Time for last 1,000,000:   21s.  Last read position: chr17:66,348,816
INFO	2016-11-10 21:39:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:39:31	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    5s.  Last read position: chr19:15,261,117
INFO	2016-11-10 21:39:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:39:41	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    9s.  Last read position: chr20:44,766,013
INFO	2016-11-10 21:39:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:39:48	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    7s.  Last read position: chrX:17,112,108
INFO	2016-11-10 21:39:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 21:39:57	MarkDuplicates	Read 20991724 records. 0 pairs never matched.
INFO	2016-11-10 21:40:04	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4203599800; totalMemory: 5978456064; maxMemory: 11453595648
INFO	2016-11-10 21:40:04	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 21:40:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 21:40:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 21:40:06	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 21:40:07	MarkDuplicates	After generateDuplicateIndexes freeMemory: 3036902960; totalMemory: 5978456064; maxMemory: 11453595648
INFO	2016-11-10 21:40:07	MarkDuplicates	Marking 2606962 records as duplicates.
INFO	2016-11-10 21:40:07	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-10 21:42:27	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:20s.  Time for last 10,000,000:  140s.  Last read position: chr9:5,415,036
INFO	2016-11-10 21:45:24	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:05:16s.  Time for last 10,000,000:  176s.  Last read position: chrX:17,112,108
INFO	2016-11-10 21:45:44	MarkDuplicates	Before output close freeMemory: 8633163608; totalMemory: 8714190848; maxMemory: 11453595648
INFO	2016-11-10 21:45:55	MarkDuplicates	After output close freeMemory: 8764171888; totalMemory: 8845262848; maxMemory: 11453595648
[Thu Nov 10 21:45:57 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 10.74 minutes.
Runtime.totalMemory()=8845262848

Num	6
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	7399

OK	false
Exit Code	3
Retries
State	KILLED
Dep.	ERROR
Cpus	4
Mem

Start	2016-11-10 20:56:29
End	2016-11-10 21:43:52
Elapsed	00:47:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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/SRR1370886_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/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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/SRR1370886_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/SRR1370886_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--------------------
27259 (process ID) old priority 0, new priority 10

Type	Name	Value
int{}	filesize	{rep1=3983963325, ctl1=11033042636}
int{}	nth_rep	{rep1=1, ctl1=4}

BigDataScript report: chipseq.bds

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