Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161110_115545_525
Start time	2016-11-10 11:55:45
Run time	01:21:29.048
Tasks executed	2
Tasks failed	2
Tasks failed names	bwa_sam rep1 markdup_bam_picard ctl1
Arguments*	[-title, SRR1370907_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370907_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	1

Thread ID	Parent	Tasks
thread_Root	None
thread_41	thread_Root	chipseq.bds.20161110_115545_525_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_10
thread_42	thread_Root	chipseq.bds.20161110_115545_525_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bwa.bwa_sam_rep1.line_140.id_10
Name	bwa_sam rep1
Thread	thread_41
PID	6639

OK	false
Exit Code	3
Retries
State	KILLED
Dep.	ERROR
Cpus	1
Mem

Start	2016-11-10 11:55:49
End	2016-11-10 12:00:54
Elapsed	00:05:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370907_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/rep1/SRR1370907_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/rep1/SRR1370907_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/qc/rep1/SRR1370907_1.flagstat.qc
Dependencies

 
# SYS command. line 142

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/SRR1370907_1/out/align/rep1/SRR1370907_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370907_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/rep1/SRR1370907_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/rep1/SRR1370907_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/qc/rep1/SRR1370907_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--------------------
9795 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.12 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.56 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.69 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.60 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.70 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.74 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.79 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.59 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.34 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.16 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.53 sec
[bwa_aln_core] refine gapped alignments... 4.01 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.08 sec
[bwa_aln_core] refine gapped alignments... 4.64 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.34 sec
[bwa_aln_core] refine gapped alignments... 4.99 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.75 sec
[bwa_aln_core] refine gapped alignments... 4.22 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.50 sec
[bwa_aln_core] refine gapped alignments... 4.91 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.40 sec
[bwa_aln_core] refine gapped alignments... 5.35 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.05 sec
[bwa_aln_core] refine gapped alignments... 5.56 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.45 sec
[bwa_aln_core] refine gapped alignments... 4.97 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.93 sec
[bwa_aln_core] refine gapped alignments... 5.59 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.67 sec
[bwa_aln_core] refine gapped alignments... 5.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.00 sec
[bwa_aln_core] refine gapped alignments... 6.32 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.98 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.73 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.27 sec
[bwa_aln_core] refine gapped alignments... 5.30 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.40 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.64 sec
[bwa_aln_core] refine gapped alignments... 5.28 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.36 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.28 sec
[bwa_aln_core] refine gapped alignments... 5.18 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.16 sec
[bwa_aln_core] refine gapped alignments... 5.37 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.12 sec
[bwa_aln_core] refine gapped alignments... 5.27 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.91 sec
[bwa_aln_core] refine gapped alignments... 5.23 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.23 sec
[bwa_aln_core] refine gapped alignments... 5.24 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.23 sec
[bwa_aln_core] refine gapped alignments... 5.18 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.21 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.21 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.17 sec
[bwa_aln_core] refine gapped alignments... 5.22 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.57 sec
[bwa_aln_core] refine gapped alignments... 4.63 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.76 sec
[bwa_aln_core] refine gapped alignments... 4.60 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.74 sec
[bwa_aln_core] refine gapped alignments... 4.60 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.62 sec
[bwa_aln_core] refine gapped alignments... 4.25 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.03 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.21 sec
[bwa_aln_core] refine gapped alignments... 3.60 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.87 sec
[bwa_aln_core] refine gapped alignments... 3.19 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.22 sec
[bwa_aln_core] refine gapped alignments... 5.07 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.35 sec
[bwa_aln_core] refine gapped alignments... 4.27 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.83 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.12 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.19 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.35 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.03 sec
[bwa_aln_core] refine gapped alignments... 4.19 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.60 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.03 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.06 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.94 sec
[bwa_aln_core] refine gapped alignments... 1.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.78 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.97 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.27 sec
[bwa_aln_core] refine gapped alignments... 1.35 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.73 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.47 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.19 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.82 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.60 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.52 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.05 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.64 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.95 sec
[bwa_aln_core] refine gapped alignments... 4.95 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.08 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.64 sec
[bwa_aln_core] refine gapped alignments... 6.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.56 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.07 sec
[bwa_aln_core] refine gapped alignments... 4.89 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.47 sec
[bwa_aln_core] refine gapped alignments... 4.34 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.08 sec
[bwa_aln_core] refine gapped alignments... 1.15 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.47 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.66 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.27 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.87 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.14 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.88 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.51 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.13 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.09 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.11 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.88 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.67 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.96 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.82 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.71 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.52 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.07 sec
[bwa_aln_core] 24688247 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/SRR1370907_1/out/align/rep1/SRR1370907_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370907_1.fastq.gz
[main] Real time: 2691.617 sec; CPU: 2529.228 sec
sambamba-sort: Unable to write to stream

Num	2
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	6640

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

Start	2016-11-10 11:55:49
End	2016-11-10 11:55:49
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc
Dependencies

 
# SYS command. line 349

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

# SYS command. line 353

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 354

 export MAX_JAVA_MEM="12G"

# SYS command. line 359

 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 368

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_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/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 380

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

   
--------------------Stdout--------------------
9792 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu Nov 10 11:56:04 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_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 11:56:04 PST 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-10 11:56:07	MarkDuplicates	Start of doWork freeMemory: 254879328; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-10 11:56:07	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 11:56:07	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-10 11:56:16	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 11:56:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:56:25	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    9s.  Last read position: chr1:41,895,424
INFO	2016-11-10 11:56:25	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 11:56:33	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    7s.  Last read position: chr1:63,396,527
INFO	2016-11-10 11:56:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:56:45	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:   11s.  Last read position: chr1:89,147,707
INFO	2016-11-10 11:56:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:56:59	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:   14s.  Last read position: chr1:115,615,553
INFO	2016-11-10 11:56:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:57:09	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    9s.  Last read position: chr1:164,468,682
INFO	2016-11-10 11:57:09	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 11:57:18	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    8s.  Last read position: chr1:189,102,252
INFO	2016-11-10 11:57:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:57:30	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   12s.  Last read position: chr1:213,979,760
INFO	2016-11-10 11:57:30	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:57:40	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:   10s.  Last read position: chr1:231,814,268
INFO	2016-11-10 11:57:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:57:46	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    5s.  Last read position: chr2:3,652,468
INFO	2016-11-10 11:57:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:57:55	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    9s.  Last read position: chr2:39,505,122
INFO	2016-11-10 11:57:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:06	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:   11s.  Last read position: chr2:73,561,393
INFO	2016-11-10 11:58:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:58:13	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    6s.  Last read position: chr2:120,526,571
INFO	2016-11-10 11:58:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:20	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    7s.  Last read position: chr2:160,316,783
INFO	2016-11-10 11:58:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:58:41	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:   20s.  Last read position: chr2:195,549,735
INFO	2016-11-10 11:58:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:58:51	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:   10s.  Last read position: chr2:230,358,034
INFO	2016-11-10 11:58:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:59:01	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    9s.  Last read position: chr3:16,305,780
INFO	2016-11-10 11:59:01	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 11:59:11	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    9s.  Last read position: chr3:49,251,279
INFO	2016-11-10 11:59:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:59:21	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:   10s.  Last read position: chr3:84,621,225
INFO	2016-11-10 11:59:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:59:33	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:   11s.  Last read position: chr3:128,121,129
INFO	2016-11-10 11:59:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:59:43	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:   10s.  Last read position: chr3:165,373,238
INFO	2016-11-10 11:59:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:59:58	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:   15s.  Last read position: chr3:195,333,247
INFO	2016-11-10 11:59:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:07	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    8s.  Last read position: chr4:37,752,582
INFO	2016-11-10 12:00:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:16	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    9s.  Last read position: chr4:81,286,306
INFO	2016-11-10 12:00:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:23	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    6s.  Last read position: chr4:119,339,736
INFO	2016-11-10 12:00:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:35	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:   12s.  Last read position: chr4:158,818,783
INFO	2016-11-10 12:00:35	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:00:41	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    5s.  Last read position: chr5:6,447,551
INFO	2016-11-10 12:00:41	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 12:00:51	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    9s.  Last read position: chr5:33,219,021
INFO	2016-11-10 12:00:51	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:01:01	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:   10s.  Last read position: chr5:60,694,078
INFO	2016-11-10 12:01:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:01:14	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:   13s.  Last read position: chr5:86,336,676
INFO	2016-11-10 12:01:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:01:21	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    6s.  Last read position: chr5:112,930,184
INFO	2016-11-10 12:01:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:01:31	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:   10s.  Last read position: chr5:136,852,889
INFO	2016-11-10 12:01:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:01:39	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:05:31s.  Time for last 1,000,000:    7s.  Last read position: chr5:160,271,193
INFO	2016-11-10 12:01:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:01:46	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    6s.  Last read position: chr6:4,126,386
INFO	2016-11-10 12:01:46	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:01:54	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    7s.  Last read position: chr6:28,666,579
INFO	2016-11-10 12:01:54	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:02:04	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:   10s.  Last read position: chr6:49,527,281
INFO	2016-11-10 12:02:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:02:14	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:06:07s.  Time for last 1,000,000:   10s.  Last read position: chr6:81,728,195
INFO	2016-11-10 12:02:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:02:21	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:06:14s.  Time for last 1,000,000:    7s.  Last read position: chr6:107,535,760
INFO	2016-11-10 12:02:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:02:29	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    7s.  Last read position: chr6:132,364,408
INFO	2016-11-10 12:02:29	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:02:35	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    6s.  Last read position: chr6:156,918,595
INFO	2016-11-10 12:02:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:02:43	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    7s.  Last read position: chr7:18,636,743
INFO	2016-11-10 12:02:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:02:56	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:   12s.  Last read position: chr7:53,850,313
INFO	2016-11-10 12:02:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:05	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    9s.  Last read position: chr7:96,503,433
INFO	2016-11-10 12:03:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:03:13	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    7s.  Last read position: chr7:120,651,846
INFO	2016-11-10 12:03:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:21	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:07:13s.  Time for last 1,000,000:    8s.  Last read position: chr7:146,401,497
INFO	2016-11-10 12:03:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:29	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    7s.  Last read position: chr8:17,030,519
INFO	2016-11-10 12:03:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:37	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    7s.  Last read position: chr8:42,750,671
INFO	2016-11-10 12:03:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:46	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    9s.  Last read position: chr8:85,385,487
INFO	2016-11-10 12:03:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:56	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    9s.  Last read position: chr8:124,358,985
INFO	2016-11-10 12:03:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:10	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:08:02s.  Time for last 1,000,000:   14s.  Last read position: chr9:18,183,883
INFO	2016-11-10 12:04:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:04:22	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:   11s.  Last read position: chr9:84,163,983
INFO	2016-11-10 12:04:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:04:34	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:08:26s.  Time for last 1,000,000:   11s.  Last read position: chr9:119,875,535
INFO	2016-11-10 12:04:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:04:49	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:08:41s.  Time for last 1,000,000:   14s.  Last read position: chr10:5,661,683
INFO	2016-11-10 12:04:49	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:04:56	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    7s.  Last read position: chr10:29,748,948
INFO	2016-11-10 12:04:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:05:04	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    7s.  Last read position: chr10:61,280,221
INFO	2016-11-10 12:05:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:10	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:09:03s.  Time for last 1,000,000:    6s.  Last read position: chr10:85,305,552
INFO	2016-11-10 12:05:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:05:19	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:09:11s.  Time for last 1,000,000:    8s.  Last read position: chr10:108,129,202
INFO	2016-11-10 12:05:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:29	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:09:21s.  Time for last 1,000,000:   10s.  Last read position: chr10:132,730,123
INFO	2016-11-10 12:05:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:05:42	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:09:34s.  Time for last 1,000,000:   13s.  Last read position: chr11:35,359,267
INFO	2016-11-10 12:05:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:47	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    5s.  Last read position: chr11:75,696,431
INFO	2016-11-10 12:05:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:05:59	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:   11s.  Last read position: chr11:114,414,621
INFO	2016-11-10 12:05:59	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:06:05	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:09:58s.  Time for last 1,000,000:    6s.  Last read position: chr12:8,900,276
INFO	2016-11-10 12:06:05	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:06:17	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:10:10s.  Time for last 1,000,000:   11s.  Last read position: chr12:38,863,889
INFO	2016-11-10 12:06:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:25	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    7s.  Last read position: chr12:60,598,824
INFO	2016-11-10 12:06:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:06:33	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:10:26s.  Time for last 1,000,000:    8s.  Last read position: chr12:88,520,538
INFO	2016-11-10 12:06:33	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:06:46	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:10:39s.  Time for last 1,000,000:   13s.  Last read position: chr12:112,268,437
INFO	2016-11-10 12:06:46	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:07:00	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:10:52s.  Time for last 1,000,000:   13s.  Last read position: chr13:23,999,632
INFO	2016-11-10 12:07:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:07:09	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:11:01s.  Time for last 1,000,000:    9s.  Last read position: chr13:51,165,870
INFO	2016-11-10 12:07:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:07:16	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:11:08s.  Time for last 1,000,000:    7s.  Last read position: chr13:88,986,369
INFO	2016-11-10 12:07:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:24	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:11:17s.  Time for last 1,000,000:    8s.  Last read position: chr14:23,149,367
INFO	2016-11-10 12:07:24	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:07:37	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:11:29s.  Time for last 1,000,000:   12s.  Last read position: chr14:58,140,905
INFO	2016-11-10 12:07:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:46	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:11:38s.  Time for last 1,000,000:    8s.  Last read position: chr14:91,912,553
INFO	2016-11-10 12:07:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:07:54	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:11:47s.  Time for last 1,000,000:    8s.  Last read position: chr15:38,895,095
INFO	2016-11-10 12:07:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:08:08	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:   13s.  Last read position: chr15:68,188,367
INFO	2016-11-10 12:08:08	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:08:19	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:12:11s.  Time for last 1,000,000:   10s.  Last read position: chr15:87,921,272
INFO	2016-11-10 12:08:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:08:33	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:12:25s.  Time for last 1,000,000:   14s.  Last read position: chr16:11,143,813
INFO	2016-11-10 12:08:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:08:48	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:12:40s.  Time for last 1,000,000:   15s.  Last read position: chr16:51,391,437
INFO	2016-11-10 12:08:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:08:59	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:12:51s.  Time for last 1,000,000:   10s.  Last read position: chr16:84,928,458
INFO	2016-11-10 12:08:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:07	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:13:00s.  Time for last 1,000,000:    8s.  Last read position: chr17:18,368,935
INFO	2016-11-10 12:09:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:09:16	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:13:08s.  Time for last 1,000,000:    8s.  Last read position: chr17:44,246,522
INFO	2016-11-10 12:09:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:26	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:13:19s.  Time for last 1,000,000:   10s.  Last read position: chr17:66,172,158
INFO	2016-11-10 12:09:26	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 12:09:34	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:13:27s.  Time for last 1,000,000:    7s.  Last read position: chr18:5,619,614
INFO	2016-11-10 12:09:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:09:44	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:13:36s.  Time for last 1,000,000:    9s.  Last read position: chr18:46,152,631
INFO	2016-11-10 12:09:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:49	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:13:42s.  Time for last 1,000,000:    5s.  Last read position: chr19:1,328,731
INFO	2016-11-10 12:09:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:09:58	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:13:51s.  Time for last 1,000,000:    9s.  Last read position: chr19:28,148,444
INFO	2016-11-10 12:09:58	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:10:08	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:14:00s.  Time for last 1,000,000:    9s.  Last read position: chr19:40,341,579
INFO	2016-11-10 12:10:08	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:10:14	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:14:06s.  Time for last 1,000,000:    6s.  Last read position: chr20:3,222,035
INFO	2016-11-10 12:10:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:10:21	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:14:13s.  Time for last 1,000,000:    7s.  Last read position: chr20:37,218,903
INFO	2016-11-10 12:10:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:10:38	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:14:31s.  Time for last 1,000,000:   17s.  Last read position: chr20:62,871,367
INFO	2016-11-10 12:10:38	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 12:10:46	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:14:39s.  Time for last 1,000,000:    8s.  Last read position: chr21:39,474,524
INFO	2016-11-10 12:10:46	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:11:00	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:14:52s.  Time for last 1,000,000:   13s.  Last read position: chr22:31,346,944
INFO	2016-11-10 12:11:00	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:11:12	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:15:04s.  Time for last 1,000,000:   11s.  Last read position: chrX:6,235,951
INFO	2016-11-10 12:11:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:11:17	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:15:10s.  Time for last 1,000,000:    5s.  Last read position: chrX:38,820,975
INFO	2016-11-10 12:11:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:11:26	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:15:18s.  Time for last 1,000,000:    8s.  Last read position: chrX:69,473,954
INFO	2016-11-10 12:11:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:11:34	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:15:26s.  Time for last 1,000,000:    7s.  Last read position: chrX:92,683,143
INFO	2016-11-10 12:11:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:11:44	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:15:36s.  Time for last 1,000,000:    9s.  Last read position: chrX:118,447,518
INFO	2016-11-10 12:11:44	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:11:56	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:15:48s.  Time for last 1,000,000:   12s.  Last read position: chrX:142,819,613
INFO	2016-11-10 12:11:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:12:03	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:15:55s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,995
INFO	2016-11-10 12:12:03	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 12:12:07	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:15:59s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,775
INFO	2016-11-10 12:12:07	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 12:12:15	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 12:12:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3061155904; totalMemory: 3088580608; maxMemory: 3817865216
INFO	2016-11-10 12:12:20	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-10 12:12:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 12:12:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 12:12:57	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 12:12:57	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2046881760; totalMemory: 3028811776; maxMemory: 3817865216
INFO	2016-11-10 12:12:57	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 12:12:57	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-10 12:15:13	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:15s.  Time for last 10,000,000:  135s.  Last read position: chr2:3,652,468
INFO	2016-11-10 12:17:35	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:38s.  Time for last 10,000,000:  142s.  Last read position: chr3:128,121,129
[Thu Nov 10 12:19:14 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 23.16 minutes.
Runtime.totalMemory()=3158310912
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
	at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:208)
	at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:331)
	at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:294)
	at htsjdk.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:194)
	at java.io.DataOutputStream.write(DataOutputStream.java:107)
	at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
	at htsjdk.samtools.util.BinaryCodec.writeByteBuffer(BinaryCodec.java:174)
	at htsjdk.samtools.util.BinaryCodec.writeUShort(BinaryCodec.java:337)
	at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:128)
	at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:127)
	at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:177)
	at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:194)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
Caused by: java.io.IOException: No space left on device
	at java.io.FileOutputStream.writeBytes(Native Method)
	at java.io.FileOutputStream.write(FileOutputStream.java:326)
	at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
	at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
	at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
	... 14 more

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, SRR1370907_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370907_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370907_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

BigDataScript report: chipseq.bds

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