Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161110_115525_836
Start time	2016-11-10 11:55:25
Run time	00:24:27.984
Tasks executed	2
Tasks failed	1
Tasks failed names	markdup_bam_picard ctl1
Arguments*	[-title, SRR1370895_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370895_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_115525_836_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_10
thread_42	thread_Root	chipseq.bds.20161110_115525_836_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	6621

OK	false
Exit Code	0
Retries
State	RUNNING
Dep.	WAIT
Cpus	1
Mem

Start	2016-11-10 11:55:28
End	2016-11-10 11:55:28
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370895_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/rep1/SRR1370895_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/rep1/SRR1370895_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/qc/rep1/SRR1370895_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/SRR1370895_1/out/align/rep1/SRR1370895_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370895_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/rep1/SRR1370895_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/rep1/SRR1370895_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/qc/rep1/SRR1370895_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--------------------
9510 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.02 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.43 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.89 sec
[bwa_aln_core] refine gapped alignments... 7.11 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.42 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.31 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.80 sec
[bwa_aln_core] refine gapped alignments... 0.41 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... 19.41 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.13 sec
[bwa_aln_core] refine gapped alignments... 3.94 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.57 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.27 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.90 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.17 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.08 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.85 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.90 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.91 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.13 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.62 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.04 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.58 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.39 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.68 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.14 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.49 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.32 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.24 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.70 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.51 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.10 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.58 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.04 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.19 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.64 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.71 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.35 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.05 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.14 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.96 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.71 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.36 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.46 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments...

Num	2
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	6624

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

Start	2016-11-10 11:55:28
End	2016-11-10 11:55:28
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_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/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_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/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_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--------------------
43376 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu Nov 10 11:55:49 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_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 11:55:49 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 11:55:49	MarkDuplicates	Start of doWork freeMemory: 254879416; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-10 11:55:49	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 11:55:49	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-10 11:56:04	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:   12s.  Last read position: chr1:22,298,551
INFO	2016-11-10 11:56:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:56:14	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    9s.  Last read position: chr1:41,895,424
INFO	2016-11-10 11:56:14	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 11:56:24	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:   10s.  Last read position: chr1:63,396,527
INFO	2016-11-10 11:56:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:56:35	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:   10s.  Last read position: chr1:89,147,707
INFO	2016-11-10 11:56:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:56:56	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:   21s.  Last read position: chr1:115,615,553
INFO	2016-11-10 11:56:56	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: 00:01:17s.  Time for last 1,000,000:   13s.  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 11:57:27	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:   18s.  Last read position: chr1:189,102,252
INFO	2016-11-10 11:57:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:57:40	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:   12s.  Last read position: chr1:213,979,760
INFO	2016-11-10 11:57:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:57:52	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:   11s.  Last read position: chr1:231,814,268
INFO	2016-11-10 11:57:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:03	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:   11s.  Last read position: chr2:3,652,468
INFO	2016-11-10 11:58:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:58:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:   10s.  Last read position: chr2:39,505,122
INFO	2016-11-10 11:58:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:21	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    7s.  Last read position: chr2:73,561,393
INFO	2016-11-10 11:58:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:58:34	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:   12s.  Last read position: chr2:120,526,571
INFO	2016-11-10 11:58:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:47	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:   13s.  Last read position: chr2:160,316,783
INFO	2016-11-10 11:58:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:59:11	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:   24s.  Last read position: chr2:195,549,735
INFO	2016-11-10 11:59:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:59:24	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:   12s.  Last read position: chr2:230,358,034
INFO	2016-11-10 11:59:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:59:35	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:   11s.  Last read position: chr3:16,305,780
INFO	2016-11-10 11:59:35	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 11:59:52	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:   16s.  Last read position: chr3:49,251,279
INFO	2016-11-10 11:59:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:08	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:   15s.  Last read position: chr3:84,621,225
INFO	2016-11-10 12:00:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:19	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:   10s.  Last read position: chr3:128,121,129
INFO	2016-11-10 12:00:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:32	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:   13s.  Last read position: chr3:165,373,238
INFO	2016-11-10 12:00:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:42	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    9s.  Last read position: chr3:195,333,247
INFO	2016-11-10 12:00:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:54	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:   12s.  Last read position: chr4:37,752,582
INFO	2016-11-10 12:00:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:01:10	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:   15s.  Last read position: chr4:81,286,306
INFO	2016-11-10 12:01:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:01:20	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    9s.  Last read position: chr4:119,339,736
INFO	2016-11-10 12:01:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:01:35	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:   14s.  Last read position: chr4:158,818,783
INFO	2016-11-10 12:01:35	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:01:50	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:   15s.  Last read position: chr5:6,447,551
INFO	2016-11-10 12:01:50	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 12:02:05	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:   14s.  Last read position: chr5:33,219,021
INFO	2016-11-10 12:02:05	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:02:15	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:   10s.  Last read position: chr5:60,694,078
INFO	2016-11-10 12:02:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:02:36	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:   20s.  Last read position: chr5:86,336,676
INFO	2016-11-10 12:02:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:02:45	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    9s.  Last read position: chr5:112,930,184
INFO	2016-11-10 12:02:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:03:02	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:   16s.  Last read position: chr5:136,852,889
INFO	2016-11-10 12:03:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:15	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:07:23s.  Time for last 1,000,000:   13s.  Last read position: chr5:160,271,193
INFO	2016-11-10 12:03:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:24	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    9s.  Last read position: chr6:4,126,386
INFO	2016-11-10 12:03:24	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:03:34	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:07:42s.  Time for last 1,000,000:   10s.  Last read position: chr6:28,666,579
INFO	2016-11-10 12:03:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:03:43	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    8s.  Last read position: chr6:49,527,281
INFO	2016-11-10 12:03:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:59	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:   16s.  Last read position: chr6:81,728,195
INFO	2016-11-10 12:03:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:14	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:08:22s.  Time for last 1,000,000:   14s.  Last read position: chr6:107,535,760
INFO	2016-11-10 12:04:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:28	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:08:36s.  Time for last 1,000,000:   14s.  Last read position: chr6:132,364,408
INFO	2016-11-10 12:04:28	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:04:44	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:   15s.  Last read position: chr6:156,918,595
INFO	2016-11-10 12:04:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:54	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:   10s.  Last read position: chr7:18,636,743
INFO	2016-11-10 12:04:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:05	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:   10s.  Last read position: chr7:53,850,313
INFO	2016-11-10 12:05:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:16	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:   11s.  Last read position: chr7:96,503,433
INFO	2016-11-10 12:05:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:05:27	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:   11s.  Last read position: chr7:120,651,846
INFO	2016-11-10 12:05:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:42	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:   14s.  Last read position: chr7:146,401,497
INFO	2016-11-10 12:05:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:56	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:10:04s.  Time for last 1,000,000:   13s.  Last read position: chr8:17,030,519
INFO	2016-11-10 12:05:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:08	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:10:16s.  Time for last 1,000,000:   12s.  Last read position: chr8:42,750,671
INFO	2016-11-10 12:06:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:24	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:   15s.  Last read position: chr8:85,385,487
INFO	2016-11-10 12:06:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:34	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:10:42s.  Time for last 1,000,000:   10s.  Last read position: chr8:124,358,985
INFO	2016-11-10 12:06:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:06:48	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:10:56s.  Time for last 1,000,000:   14s.  Last read position: chr9:18,183,883
INFO	2016-11-10 12:06:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:07:01	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:11:09s.  Time for last 1,000,000:   13s.  Last read position: chr9:84,163,983
INFO	2016-11-10 12:07:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:07:15	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:11:23s.  Time for last 1,000,000:   13s.  Last read position: chr9:119,875,535
INFO	2016-11-10 12:07:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:23	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:11:31s.  Time for last 1,000,000:    8s.  Last read position: chr10:5,661,683
INFO	2016-11-10 12:07:23	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:07:39	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:11:47s.  Time for last 1,000,000:   15s.  Last read position: chr10:29,748,948
INFO	2016-11-10 12:07:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:07:49	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:   10s.  Last read position: chr10:61,280,221
INFO	2016-11-10 12:07:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:59	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:12:07s.  Time for last 1,000,000:   10s.  Last read position: chr10:85,305,552
INFO	2016-11-10 12:07:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:08:11	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:12:19s.  Time for last 1,000,000:   11s.  Last read position: chr10:108,129,202
INFO	2016-11-10 12:08:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:08:29	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:12:37s.  Time for last 1,000,000:   17s.  Last read position: chr10:132,730,123
INFO	2016-11-10 12:08:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:08:53	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:13:01s.  Time for last 1,000,000:   24s.  Last read position: chr11:35,359,267
INFO	2016-11-10 12:08:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:09:03	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:13:11s.  Time for last 1,000,000:   10s.  Last read position: chr11:75,696,431
INFO	2016-11-10 12:09:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:14	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:13:22s.  Time for last 1,000,000:   10s.  Last read position: chr11:114,414,621
INFO	2016-11-10 12:09:14	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:09:26	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:13:34s.  Time for last 1,000,000:   11s.  Last read position: chr12:8,900,276
INFO	2016-11-10 12:09:26	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:09:37	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:13:45s.  Time for last 1,000,000:   11s.  Last read position: chr12:38,863,889
INFO	2016-11-10 12:09:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:09:50	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:13:58s.  Time for last 1,000,000:   12s.  Last read position: chr12:60,598,824
INFO	2016-11-10 12:09:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:10:03	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:14:11s.  Time for last 1,000,000:   12s.  Last read position: chr12:88,520,538
INFO	2016-11-10 12:10:03	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:10:14	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:14:22s.  Time for last 1,000,000:   10s.  Last read position: chr12:112,268,437
INFO	2016-11-10 12:10:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:10:26	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:14:34s.  Time for last 1,000,000:   12s.  Last read position: chr13:23,999,632
INFO	2016-11-10 12:10:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:10:38	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:14:46s.  Time for last 1,000,000:   12s.  Last read position: chr13:51,165,870
INFO	2016-11-10 12:10:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:10:47	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:14:55s.  Time for last 1,000,000:    9s.  Last read position: chr13:88,986,369
INFO	2016-11-10 12:10:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:11:02	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:15:10s.  Time for last 1,000,000:   14s.  Last read position: chr14:23,149,367
INFO	2016-11-10 12:11:02	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:11:12	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:15:20s.  Time for last 1,000,000:   10s.  Last read position: chr14:58,140,905
INFO	2016-11-10 12:11:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:11:23	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:15:31s.  Time for last 1,000,000:   10s.  Last read position: chr14:91,912,553
INFO	2016-11-10 12:11:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:11:35	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:15:43s.  Time for last 1,000,000:   12s.  Last read position: chr15:38,895,095
INFO	2016-11-10 12:11:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:11:54	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:16:02s.  Time for last 1,000,000:   18s.  Last read position: chr15:68,188,367
INFO	2016-11-10 12:11:54	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:12:04	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:16:12s.  Time for last 1,000,000:   10s.  Last read position: chr15:87,921,272
INFO	2016-11-10 12:12:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:12:17	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:16:25s.  Time for last 1,000,000:   12s.  Last read position: chr16:11,143,813
INFO	2016-11-10 12:12:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:12:30	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:16:38s.  Time for last 1,000,000:   13s.  Last read position: chr16:51,391,437
INFO	2016-11-10 12:12:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:12:44	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:16:52s.  Time for last 1,000,000:   13s.  Last read position: chr16:84,928,458
INFO	2016-11-10 12:12:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:12:55	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:17:03s.  Time for last 1,000,000:   10s.  Last read position: chr17:18,368,935
INFO	2016-11-10 12:12:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:13:03	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:17:11s.  Time for last 1,000,000:    7s.  Last read position: chr17:44,246,522
INFO	2016-11-10 12:13:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:13:11	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:17:19s.  Time for last 1,000,000:    8s.  Last read position: chr17:66,172,158
INFO	2016-11-10 12:13:11	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 12:13:25	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:17:33s.  Time for last 1,000,000:   13s.  Last read position: chr18:5,619,614
INFO	2016-11-10 12:13:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:13:35	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:17:43s.  Time for last 1,000,000:    9s.  Last read position: chr18:46,152,631
INFO	2016-11-10 12:13:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:13:50	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:17:58s.  Time for last 1,000,000:   15s.  Last read position: chr19:1,328,731
INFO	2016-11-10 12:13:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:14:00	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:18:08s.  Time for last 1,000,000:    9s.  Last read position: chr19:28,148,444
INFO	2016-11-10 12:14:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:14:09	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:18:17s.  Time for last 1,000,000:    9s.  Last read position: chr19:40,341,579
INFO	2016-11-10 12:14:09	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:14:27	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:18:35s.  Time for last 1,000,000:   17s.  Last read position: chr20:3,222,035
INFO	2016-11-10 12:14:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:14:43	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:18:51s.  Time for last 1,000,000:   16s.  Last read position: chr20:37,218,903
INFO	2016-11-10 12:14:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:15:05	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:19:13s.  Time for last 1,000,000:   21s.  Last read position: chr20:62,871,367
INFO	2016-11-10 12:15:05	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 12:15:15	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:19:23s.  Time for last 1,000,000:   10s.  Last read position: chr21:39,474,524
INFO	2016-11-10 12:15:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:15:29	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:19:37s.  Time for last 1,000,000:   14s.  Last read position: chr22:31,346,944
INFO	2016-11-10 12:15:29	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:15:42	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:19:50s.  Time for last 1,000,000:   12s.  Last read position: chrX:6,235,951
INFO	2016-11-10 12:15:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:15:52	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:20:00s.  Time for last 1,000,000:    9s.  Last read position: chrX:38,820,975
INFO	2016-11-10 12:15:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:16:04	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:20:12s.  Time for last 1,000,000:   12s.  Last read position: chrX:69,473,954
INFO	2016-11-10 12:16:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:16:18	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:20:26s.  Time for last 1,000,000:   13s.  Last read position: chrX:92,683,143
INFO	2016-11-10 12:16:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:16:28	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:20:36s.  Time for last 1,000,000:    9s.  Last read position: chrX:118,447,518
INFO	2016-11-10 12:16:28	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:16:37	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:20:45s.  Time for last 1,000,000:    8s.  Last read position: chrX:142,819,613
INFO	2016-11-10 12:16:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:16:43	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:20:51s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,995
INFO	2016-11-10 12:16:43	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 12:16:53	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:21:01s.  Time for last 1,000,000:   10s.  Last read position: chrM:11,775
INFO	2016-11-10 12:16:53	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 12:17:00	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 12:17:06	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3143369912; totalMemory: 3170893824; maxMemory: 3817865216
INFO	2016-11-10 12:17:06	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-10 12:17:06	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 12:17:25	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 12:17:52	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 12:17:52	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2129215304; totalMemory: 3111124992; maxMemory: 3817865216
INFO	2016-11-10 12:17:52	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 12:17:52	MarkDuplicates	Found 42648 optical duplicate clusters.
[Thu Nov 10 12:19:17 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 23.47 minutes.
Runtime.totalMemory()=3188719616
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/SRR1370895_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.writeBytes(BinaryCodec.java:198)
	at htsjdk.samtools.util.BinaryCodec.writeString(BinaryCodec.java:305)
	at htsjdk.samtools.util.BinaryCodec.writeString(BinaryCodec.java:292)
	at htsjdk.samtools.BinaryTagCodec.writeTag(BinaryTagCodec.java:193)
	at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:163)
	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)
	... 16 more

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 6624
exec_file:                  job_scripts/6624
submission_time:            Thu Nov 10 11:55:28 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370895_1
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE

BigDataScript report: chipseq.bds

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Task details