Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170128_225226_744
Start time	2017-01-28 22:52:26
Run time	01:46:28.393
Tasks executed	26
Tasks failed	0
Tasks failed names
Arguments*	[-title, H2AK119Ub1, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz, -final_stage, idr, -histone, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170128_225226_744/task.callpeak_macs2.macs2_rep1.line_71.id_25 chipseq.bds.20170128_225226_744/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26 chipseq.bds.20170128_225226_744/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27 chipseq.bds.20170128_225226_744/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28 chipseq.bds.20170128_225226_744/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29 chipseq.bds.20170128_225226_744/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30 chipseq.bds.20170128_225226_744/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31 chipseq.bds.20170128_225226_744/task.report.peak2hammock.line_412.id_32 chipseq.bds.20170128_225226_744/task.report.peak2hammock.line_412.id_33 chipseq.bds.20170128_225226_744/task.graphviz.report.line_97.id_34 chipseq.bds.20170128_225226_744/task.report.pdf2png.line_379.id_39
thread_41	thread_Root	chipseq.bds.20170128_225226_744_parallel_41/task.align_bwa.bwa_aln_rep1.line_111.id_10 chipseq.bds.20170128_225226_744_parallel_41/task.align_bwa.bwa_sam_rep1.line_143.id_12 chipseq.bds.20170128_225226_744_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_14 chipseq.bds.20170128_225226_744_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_15 chipseq.bds.20170128_225226_744_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_16 chipseq.bds.20170128_225226_744_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_17 chipseq.bds.20170128_225226_744_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_19 chipseq.bds.20170128_225226_744_parallel_41/task.postalign_bed.spr_rep1.line_255.id_20 chipseq.bds.20170128_225226_744_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_22
thread_42	thread_Root	chipseq.bds.20170128_225226_744_parallel_42/task.align_bwa.bwa_aln_ctl1.line_111.id_11 chipseq.bds.20170128_225226_744_parallel_42/task.align_bwa.bwa_sam_ctl1.line_143.id_13 chipseq.bds.20170128_225226_744_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_18 chipseq.bds.20170128_225226_744_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_21 chipseq.bds.20170128_225226_744_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_23 chipseq.bds.20170128_225226_744_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_24

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bwa.bwa_aln_rep1.line_111.id_10
Name	bwa_aln rep1
Thread	thread_41
PID	35876

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-28 22:52:29
End	2017-01-28 23:16:01
Elapsed	00:23:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.sai
Dependencies

 
# SYS command. line 113

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

# SYS command. line 116

 bwa aln -q 5 -l 32 -k 2 -t 3 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.sai

# SYS command. line 118

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

   
--------------------Stdout--------------------
52396 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.74 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.94 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 32892196 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 3 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz
[main] Real time: 1382.147 sec; CPU: 3921.460 sec

Num	2
ID	task.align_bwa.bwa_aln_ctl1.line_111.id_11
Name	bwa_aln ctl1
Thread	thread_42
PID	35877

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

Start	2017-01-28 22:52:29
End	2017-01-28 23:35:18
Elapsed	00:42:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.sai
Dependencies

 
# SYS command. line 113

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

# SYS command. line 116

 bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.sai

# SYS command. line 118

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

   
--------------------Stdout--------------------
52395 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.03 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.29 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.80 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.63 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.78 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.78 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.18 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.85 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 23308162 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz
[main] Real time: 2538.865 sec; CPU: 2534.884 sec

Num	3
ID	task.align_bwa.bwa_sam_rep1.line_143.id_12
Name	bwa_sam rep1
Thread	thread_41
PID	35897

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-28 23:16:02
End	2017-01-28 23:35:43
Elapsed	00:19:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.flagstat.qc
Dependencies

 
# SYS command. line 145

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

# SYS command. line 150

 bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.bam

# SYS command. line 152

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.flagstat.qc

# SYS command. line 154

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

   
--------------------Stdout--------------------
18705 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.38 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.92 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.51 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.69 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.05 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.43 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.95 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.93 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.86 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.87 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.79 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.78 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.09 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.76 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.03 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.27 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.76 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.21 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.86 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.51 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 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... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.08 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.52 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.00 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.45 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.65 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.00 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.80 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.68 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.69 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.63 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.19 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.05 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.06 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.07 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.78 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.24 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.57 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.62 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.30 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.55 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.60 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.88 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.49 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.65 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.86 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.18 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.60 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.23 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.85 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.54 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.35 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 32892196 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/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz
[main] Real time: 985.001 sec; CPU: 935.756 sec

Num	4
ID	task.align_bwa.bwa_sam_ctl1.line_143.id_13
Name	bwa_sam ctl1
Thread	thread_42
PID	35907

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

Start	2017-01-28 23:35:19
End	2017-01-28 23:50:09
Elapsed	00:14:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.flagstat.qc
Dependencies

 
# SYS command. line 145

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

# SYS command. line 150

 bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.bam

# SYS command. line 152

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.flagstat.qc

# SYS command. line 154

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

   
--------------------Stdout--------------------
25960 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.36 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.79 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.64 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.83 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.93 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.39 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.22 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.08 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.25 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.27 sec
[bwa_aln_core] refine gapped alignments... 1.73 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.43 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.72 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.30 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.46 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.81 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.51 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.32 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.65 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.88 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.24 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.62 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.72 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.85 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.21 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.26 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 19398656 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... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.89 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 23308162 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/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz
[main] Real time: 592.159 sec; CPU: 539.956 sec

Num	5
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_14
Name	dedup_bam_1 rep1
Thread	thread_41
PID	35908

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-28 23:35:45
End	2017-01-28 23:39:01
Elapsed	00:03:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.filt.bam
Dependencies

 
# SYS command. line 97

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

# SYS command. line 105

 if [[ 0 > 0 ]]; then \
				sambamba sort -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.bam | \
			    	sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.filt.bam; \
			    fi

# SYS command. line 116

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

   
--------------------Stdout--------------------
27792 (process ID) old priority 0, new priority 10

Num	6
ID	task.postalign_bam.markdup_bam_picard_rep1.line_348.id_15
Name	markdup_bam_picard rep1
Thread	thread_41
PID	35910

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

Start	2017-01-28 23:39:03
End	2017-01-28 23:43:35
Elapsed	00:04:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.dup.qc
Dependencies

 
# SYS command. line 350

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

# SYS command. line 354

 export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"

# SYS command. line 360

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 369

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 381

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

   
--------------------Stdout--------------------
38543 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sat Jan 28 23:39:21 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.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
[Sat Jan 28 23:39:21 PST 2017] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-28 23:39:21	MarkDuplicates	Start of doWork freeMemory: 254879520; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-28 23:39:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-28 23:39:21	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-28 23:39:21	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR393682.14050264'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2017-01-28 23:39:25	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:65,135,470
INFO	2017-01-28 23:39:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:27	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    2s.  Last read position: chr1:227,162,724
INFO	2017-01-28 23:39:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:30	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    3s.  Last read position: chr2:78,668,157
INFO	2017-01-28 23:39:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:33	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    2s.  Last read position: chr2:234,304,074
INFO	2017-01-28 23:39:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:35	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    2s.  Last read position: chr3:176,514,627
INFO	2017-01-28 23:39:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:38	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    2s.  Last read position: chr5:9,723,567
INFO	2017-01-28 23:39:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:40	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    2s.  Last read position: chr5:163,734,777
INFO	2017-01-28 23:39:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:43	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr6:110,268,640
INFO	2017-01-28 23:39:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:46	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    3s.  Last read position: chr7:92,446,608
INFO	2017-01-28 23:39:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:49	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    2s.  Last read position: chr8:60,459,380
INFO	2017-01-28 23:39:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:51	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    2s.  Last read position: chr9:93,065,803
INFO	2017-01-28 23:39:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:54	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    2s.  Last read position: chr10:23,655,136
INFO	2017-01-28 23:39:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:56	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    2s.  Last read position: chr10:113,058,741
INFO	2017-01-28 23:39:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:39:59	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    2s.  Last read position: chr11:94,732,753
INFO	2017-01-28 23:39:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:01	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    2s.  Last read position: chr12:104,955,033
INFO	2017-01-28 23:40:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:05	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    4s.  Last read position: chr14:62,371,837
INFO	2017-01-28 23:40:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:08	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    2s.  Last read position: chr15:85,380,298
INFO	2017-01-28 23:40:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:10	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    2s.  Last read position: chr17:5,304,543
INFO	2017-01-28 23:40:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:13	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    2s.  Last read position: chr18:933,871
INFO	2017-01-28 23:40:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:15	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    2s.  Last read position: chr19:19,549,720
INFO	2017-01-28 23:40:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:17	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chr20:59,342,738
INFO	2017-01-28 23:40:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:22	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    5s.  Last read position: chrX:9,153,778
INFO	2017-01-28 23:40:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:24	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    2s.  Last read position: chrX:62,565,611
INFO	2017-01-28 23:40:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:27	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    2s.  Last read position: chrX:112,229,386
INFO	2017-01-28 23:40:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:40:30	MarkDuplicates	Read 24966434 records. 0 pairs never matched.
INFO	2017-01-28 23:40:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3253088528; totalMemory: 5261754368; maxMemory: 11453595648
INFO	2017-01-28 23:40:33	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-28 23:40:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-28 23:40:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-28 23:40:36	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-28 23:40:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5203684784; totalMemory: 8125415424; maxMemory: 11453595648
INFO	2017-01-28 23:40:37	MarkDuplicates	Marking 474508 records as duplicates.
INFO	2017-01-28 23:40:37	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-28 23:41:46	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:09s.  Time for last 10,000,000:   69s.  Last read position: chr8:60,459,380
INFO	2017-01-28 23:42:58	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:21s.  Time for last 10,000,000:   71s.  Last read position: chr19:19,549,720
INFO	2017-01-28 23:43:34	MarkDuplicates	Before output close freeMemory: 8166117224; totalMemory: 8230273024; maxMemory: 11453595648
INFO	2017-01-28 23:43:34	MarkDuplicates	After output close freeMemory: 7751404256; totalMemory: 7815561216; maxMemory: 11453595648
[Sat Jan 28 23:43:34 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.22 minutes.
Runtime.totalMemory()=7815561216

Num	7
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_16
Name	dedup_bam_2 rep1
Thread	thread_41
PID	35913

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-28 23:43:36
End	2017-01-28 23:49:29
Elapsed	00:05:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.pbc.qc
Dependencies

 
# SYS command. line 146

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

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.bam

# SYS command. line 153

 sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.pbc.qc

# SYS command. line 169

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

   
--------------------Stdout--------------------
52946 (process ID) old priority 0, new priority 10

Num	8
ID	task.postalign_bam.bam_to_tag_rep1.line_505.id_17
Name	bam_to_tag rep1
Thread	thread_41
PID	35920

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

Start	2017-01-28 23:49:31
End	2017-01-28 23:51:45
Elapsed	00:02:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 507

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

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

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

   
--------------------Stdout--------------------
58795 (process ID) old priority 0, new priority 10

Num	9
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_18
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	35921

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

Start	2017-01-28 23:50:11
End	2017-01-28 23:54:15
Elapsed	00:04:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.filt.bam
Dependencies

 
# SYS command. line 97

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

# SYS command. line 105

 if [[ 0 > 0 ]]; then \
				sambamba sort -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.filt.bam; \
			    fi

# SYS command. line 116

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

   
--------------------Stdout--------------------
18715 (process ID) old priority 0, new priority 10

Num	10
ID	task.postalign_bed.subsample_tag_rep1.line_45.id_19
Name	subsample_tag rep1
Thread	thread_41
PID	35924

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

Start	2017-01-28 23:51:47
End	2017-01-28 23:53:06
Elapsed	00:01:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.15M.tagAlign.gz
Dependencies

 
# SYS command. line 47

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

# SYS command. line 50

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.15M.tagAlign.gz

# SYS command. line 53

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

   
--------------------Stdout--------------------
25004 (process ID) old priority 0, new priority 10
Waiting for 26 seconds.

Num	11
ID	task.postalign_bed.spr_rep1.line_255.id_20
Name	spr rep1
Thread	thread_41
PID	35925

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

Start	2017-01-28 23:51:48
End	2017-01-28 23:54:19
Elapsed	00:02:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz
Dependencies

 
# SYS command. line 257

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

# SYS command. line 260

 nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz | wc -l )

# SYS command. line 261

 nlines=$(( (nlines + 1) / 2 ))

# SYS command. line 265

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.01

# SYS command. line 273

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

   
--------------------Stdout--------------------
58984 (process ID) old priority 0, new priority 10

Num	12
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_21
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	35930

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

Start	2017-01-28 23:54:17
End	2017-01-29 00:01:06
Elapsed	00:06:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.dup.qc
Dependencies

 
# SYS command. line 350

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

# SYS command. line 354

 export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"

# SYS command. line 360

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 369

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 381

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

   
--------------------Stdout--------------------
59270 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sat Jan 28 23:54:41 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.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
[Sat Jan 28 23:54:41 PST 2017] Executing as imk1@wotan on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-28 23:54:41	MarkDuplicates	Start of doWork freeMemory: 254878056; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-28 23:54:41	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-28 23:54:41	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-28 23:54:41	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR393672.1309074'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2017-01-28 23:54:51	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position: chr1:181,095,425
INFO	2017-01-28 23:54:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:54:58	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    6s.  Last read position: chr2:69,860,458
INFO	2017-01-28 23:54:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:03	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    5s.  Last read position: chr2:220,994,596
INFO	2017-01-28 23:55:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:09	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    5s.  Last read position: chr3:173,718,287
INFO	2017-01-28 23:55:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:16	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    6s.  Last read position: chr4:181,362,740
INFO	2017-01-28 23:55:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:21	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    5s.  Last read position: chr5:124,420,244
INFO	2017-01-28 23:55:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:26	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    4s.  Last read position: chr6:96,080,175
INFO	2017-01-28 23:55:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:31	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    5s.  Last read position: chr7:87,713,109
INFO	2017-01-28 23:55:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:39	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    8s.  Last read position: chr8:113,686,002
INFO	2017-01-28 23:55:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:45	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    5s.  Last read position: chr10:19,785,342
INFO	2017-01-28 23:55:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:51	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    5s.  Last read position: chr11:11,476,823
INFO	2017-01-28 23:55:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:55:56	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    5s.  Last read position: chr12:71,219,873
INFO	2017-01-28 23:55:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:56:01	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    4s.  Last read position: chr14:35,956,138
INFO	2017-01-28 23:56:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:56:07	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    5s.  Last read position: chr16:13,786,650
INFO	2017-01-28 23:56:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:56:17	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:   10s.  Last read position: chr18:54,745,907
INFO	2017-01-28 23:56:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:56:24	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    6s.  Last read position: chr22:24,153,676
INFO	2017-01-28 23:56:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:56:28	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    4s.  Last read position: chrX:107,570,497
INFO	2017-01-28 23:56:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-28 23:56:32	MarkDuplicates	Read 17496407 records. 0 pairs never matched.
INFO	2017-01-28 23:56:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2871043984; totalMemory: 4396154880; maxMemory: 11453595648
INFO	2017-01-28 23:56:37	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-28 23:56:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-28 23:56:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-28 23:56:46	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-28 23:56:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 4353330920; totalMemory: 7269777408; maxMemory: 11453595648
INFO	2017-01-28 23:56:48	MarkDuplicates	Marking 3759595 records as duplicates.
INFO	2017-01-28 23:56:48	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-28 23:59:11	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:23s.  Time for last 10,000,000:  143s.  Last read position: chr10:19,785,342
INFO	2017-01-29 00:01:04	MarkDuplicates	Before output close freeMemory: 7855879184; totalMemory: 7922515968; maxMemory: 11453595648
INFO	2017-01-29 00:01:04	MarkDuplicates	After output close freeMemory: 7762554760; totalMemory: 7829192704; maxMemory: 11453595648
[Sun Jan 29 00:01:04 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.40 minutes.
Runtime.totalMemory()=7829192704

Num	13
ID	task.postalign_bed.xcor_rep1.line_212.id_22
Name	xcor rep1
Thread	thread_41
PID	35931

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2017-01-28 23:54:20
End	2017-01-29 00:04:00
Elapsed	00:09:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.plot.pdf
Dependencies

 
# SYS command. line 214

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

# SYS command. line 217

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

# SYS command. line 223

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.15M.tagAlign.gz -p=3 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.qc

# SYS command. line 229

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

   
--------------------Stdout--------------------
34132 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.15M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 3 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.15M.tagAlign.gz 
opened /tmp/35931.1.q/RtmpStoJu2/SRR393682.nodup.15M.tagAlign871424bc60d6
done. read 15000000 fragments
ChIP data read length 46 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1966924 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.208325819090575,0.208261286054513,0.208172070874806 
Top 3 estimates for fragment length 215,225,240 
Window half size 610 
Phantom peak location 45 
Phantom peak Correlation 0.2066525 
Normalized Strand cross-correlation coefficient (NSC) 1.059145 
Relative Strand cross-correlation Coefficient (RSC) 1.167997 
Phantom Peak Quality Tag 1 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools

Num	14
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_23
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	35943

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

Start	2017-01-29 00:01:07
End	2017-01-29 00:04:36
Elapsed	00:03:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.nodup.pbc.qc
Dependencies

 
# SYS command. line 146

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

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/ctl1/SRR393672.nodup.pbc.qc

# SYS command. line 169

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

   
--------------------Stdout--------------------
56868 (process ID) old priority 0, new priority 10

Num	15
ID	task.postalign_bam.bam_to_tag_ctl1.line_505.id_24
Name	bam_to_tag ctl1
Thread	thread_42
PID	35946

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

Start	2017-01-29 00:04:38
End	2017-01-29 00:05:52
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 507

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

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

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

   
--------------------Stdout--------------------
12015 (process ID) old priority 0, new priority 10

Waiting for 32 seconds.

Num	16
ID	task.callpeak_macs2.macs2_rep1.line_71.id_25
Name	macs2 rep1
Thread	thread_Root
PID	35947

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

Start	2017-01-29 00:05:54
End	2017-01-29 00:35:45
Elapsed	00:29:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/signal/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/signal/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 73

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

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 215 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1 -o "SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/signal/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1 -o "SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/signal/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

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

   
--------------------Stdout--------------------
16314 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:06:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 00:06:08: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:06:08: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:06:09:  1000000 
INFO  @ Sun, 29 Jan 2017 00:06:11:  2000000 
INFO  @ Sun, 29 Jan 2017 00:06:12:  3000000 
INFO  @ Sun, 29 Jan 2017 00:06:14:  4000000 
INFO  @ Sun, 29 Jan 2017 00:06:15:  5000000 
INFO  @ Sun, 29 Jan 2017 00:06:16:  6000000 
INFO  @ Sun, 29 Jan 2017 00:06:18:  7000000 
INFO  @ Sun, 29 Jan 2017 00:06:19:  8000000 
INFO  @ Sun, 29 Jan 2017 00:06:21:  9000000 
INFO  @ Sun, 29 Jan 2017 00:06:22:  10000000 
INFO  @ Sun, 29 Jan 2017 00:06:24:  11000000 
INFO  @ Sun, 29 Jan 2017 00:06:25:  12000000 
INFO  @ Sun, 29 Jan 2017 00:06:26:  13000000 
INFO  @ Sun, 29 Jan 2017 00:06:28:  14000000 
INFO  @ Sun, 29 Jan 2017 00:06:29:  15000000 
INFO  @ Sun, 29 Jan 2017 00:06:30:  16000000 
INFO  @ Sun, 29 Jan 2017 00:06:32:  17000000 
INFO  @ Sun, 29 Jan 2017 00:06:33:  18000000 
INFO  @ Sun, 29 Jan 2017 00:06:35:  19000000 
INFO  @ Sun, 29 Jan 2017 00:06:36:  20000000 
INFO  @ Sun, 29 Jan 2017 00:06:37:  21000000 
INFO  @ Sun, 29 Jan 2017 00:06:39:  22000000 
INFO  @ Sun, 29 Jan 2017 00:06:40:  23000000 
INFO  @ Sun, 29 Jan 2017 00:06:42:  24000000 
INFO  @ Sun, 29 Jan 2017 00:06:43: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:06:44:  1000000 
INFO  @ Sun, 29 Jan 2017 00:06:45:  2000000 
INFO  @ Sun, 29 Jan 2017 00:06:47:  3000000 
INFO  @ Sun, 29 Jan 2017 00:06:48:  4000000 
INFO  @ Sun, 29 Jan 2017 00:06:50:  5000000 
INFO  @ Sun, 29 Jan 2017 00:06:51:  6000000 
INFO  @ Sun, 29 Jan 2017 00:06:52:  7000000 
INFO  @ Sun, 29 Jan 2017 00:06:54:  8000000 
INFO  @ Sun, 29 Jan 2017 00:06:55:  9000000 
INFO  @ Sun, 29 Jan 2017 00:06:57:  10000000 
INFO  @ Sun, 29 Jan 2017 00:06:58:  11000000 
INFO  @ Sun, 29 Jan 2017 00:06:59:  12000000 
INFO  @ Sun, 29 Jan 2017 00:07:01:  13000000 
INFO  @ Sun, 29 Jan 2017 00:07:02: #1 tag size is determined as 43 bps 
INFO  @ Sun, 29 Jan 2017 00:07:02: #1 tag size = 43 
INFO  @ Sun, 29 Jan 2017 00:07:02: #1  total tags in treatment: 24491926 
INFO  @ Sun, 29 Jan 2017 00:07:02: #1  total tags in control: 13736812 
INFO  @ Sun, 29 Jan 2017 00:07:02: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:07:02: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:07:02: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:07:02: #2 Use 215 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:07:02: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:07:02: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:07:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:08:09: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:08:09: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:08:09: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:08:09: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:08:09: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:11:02: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:11:03: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:11:04: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:11:04: Done! 
INFO  @ Sun, 29 Jan 2017 00:11:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 215 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/rep1/SRR393682.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 00:11:08: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:11:08: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:11:10:  1000000 
INFO  @ Sun, 29 Jan 2017 00:11:11:  2000000 
INFO  @ Sun, 29 Jan 2017 00:11:13:  3000000 
INFO  @ Sun, 29 Jan 2017 00:11:14:  4000000 
INFO  @ Sun, 29 Jan 2017 00:11:16:  5000000 
INFO  @ Sun, 29 Jan 2017 00:11:17:  6000000 
INFO  @ Sun, 29 Jan 2017 00:11:18:  7000000 
INFO  @ Sun, 29 Jan 2017 00:11:20:  8000000 
INFO  @ Sun, 29 Jan 2017 00:11:21:  9000000 
INFO  @ Sun, 29 Jan 2017 00:11:23:  10000000 
INFO  @ Sun, 29 Jan 2017 00:11:24:  11000000 
INFO  @ Sun, 29 Jan 2017 00:11:25:  12000000 
INFO  @ Sun, 29 Jan 2017 00:11:27:  13000000 
INFO  @ Sun, 29 Jan 2017 00:11:28:  14000000 
INFO  @ Sun, 29 Jan 2017 00:11:30:  15000000 
INFO  @ Sun, 29 Jan 2017 00:11:31:  16000000 
INFO  @ Sun, 29 Jan 2017 00:11:33:  17000000 
INFO  @ Sun, 29 Jan 2017 00:11:34:  18000000 
INFO  @ Sun, 29 Jan 2017 00:11:35:  19000000 
INFO  @ Sun, 29 Jan 2017 00:11:37:  20000000 
INFO  @ Sun, 29 Jan 2017 00:11:38:  21000000 
INFO  @ Sun, 29 Jan 2017 00:11:40:  22000000 
INFO  @ Sun, 29 Jan 2017 00:11:41:  23000000 
INFO  @ Sun, 29 Jan 2017 00:11:42:  24000000 
INFO  @ Sun, 29 Jan 2017 00:11:43: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:11:45:  1000000 
INFO  @ Sun, 29 Jan 2017 00:11:46:  2000000 
INFO  @ Sun, 29 Jan 2017 00:11:48:  3000000 
INFO  @ Sun, 29 Jan 2017 00:11:49:  4000000 
INFO  @ Sun, 29 Jan 2017 00:11:50:  5000000 
INFO  @ Sun, 29 Jan 2017 00:11:52:  6000000 
INFO  @ Sun, 29 Jan 2017 00:11:53:  7000000 
INFO  @ Sun, 29 Jan 2017 00:11:55:  8000000 
INFO  @ Sun, 29 Jan 2017 00:11:56:  9000000 
INFO  @ Sun, 29 Jan 2017 00:11:57:  10000000 
INFO  @ Sun, 29 Jan 2017 00:11:59:  11000000 
INFO  @ Sun, 29 Jan 2017 00:12:01:  12000000 
INFO  @ Sun, 29 Jan 2017 00:12:02:  13000000 
INFO  @ Sun, 29 Jan 2017 00:12:04: #1 tag size is determined as 43 bps 
INFO  @ Sun, 29 Jan 2017 00:12:04: #1 tag size = 43 
INFO  @ Sun, 29 Jan 2017 00:12:04: #1  total tags in treatment: 24491926 
INFO  @ Sun, 29 Jan 2017 00:12:04: #1  total tags in control: 13736812 
INFO  @ Sun, 29 Jan 2017 00:12:04: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:12:04: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:12:04: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:12:04: #2 Use 215 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:12:04: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:12:04: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:12:04: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:13:18: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:14:52: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:14:54: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:14:55: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:14:55: Done! 
INFO  @ Sun, 29 Jan 2017 00:15:02: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:15:58: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:16:36: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 00:17:07: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 29 Jan 2017 00:20:00: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 00:21:59: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_FE.bdg'! 
INFO  @ Sun, 29 Jan 2017 00:26:04: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:26:52: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:27:27: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 00:27:55: Values in your input bedGraph files will be multiplied by 13.736812 ... 
INFO  @ Sun, 29 Jan 2017 00:30:43: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Sun, 29 Jan 2017 00:31:07: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 00:32:31: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign_ppois.bdg'!

Num	17
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26
Name	macs2 rep1-pr1
Thread	thread_Root
PID	35948

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

Start	2017-01-29 00:05:55
End	2017-01-29 00:13:02
Elapsed	00:07:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

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

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 215 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

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

   
--------------------Stdout--------------------
16315 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:06:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 00:06:08: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:06:08: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:06:10:  1000000 
INFO  @ Sun, 29 Jan 2017 00:06:11:  2000000 
INFO  @ Sun, 29 Jan 2017 00:06:13:  3000000 
INFO  @ Sun, 29 Jan 2017 00:06:14:  4000000 
INFO  @ Sun, 29 Jan 2017 00:06:16:  5000000 
INFO  @ Sun, 29 Jan 2017 00:06:17:  6000000 
INFO  @ Sun, 29 Jan 2017 00:06:19:  7000000 
INFO  @ Sun, 29 Jan 2017 00:06:20:  8000000 
INFO  @ Sun, 29 Jan 2017 00:06:22:  9000000 
INFO  @ Sun, 29 Jan 2017 00:06:23:  10000000 
INFO  @ Sun, 29 Jan 2017 00:06:25:  11000000 
INFO  @ Sun, 29 Jan 2017 00:06:26:  12000000 
INFO  @ Sun, 29 Jan 2017 00:06:27: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:06:29:  1000000 
INFO  @ Sun, 29 Jan 2017 00:06:30:  2000000 
INFO  @ Sun, 29 Jan 2017 00:06:32:  3000000 
INFO  @ Sun, 29 Jan 2017 00:06:33:  4000000 
INFO  @ Sun, 29 Jan 2017 00:06:34:  5000000 
INFO  @ Sun, 29 Jan 2017 00:06:36:  6000000 
INFO  @ Sun, 29 Jan 2017 00:06:37:  7000000 
INFO  @ Sun, 29 Jan 2017 00:06:39:  8000000 
INFO  @ Sun, 29 Jan 2017 00:06:40:  9000000 
INFO  @ Sun, 29 Jan 2017 00:06:41:  10000000 
INFO  @ Sun, 29 Jan 2017 00:06:43:  11000000 
INFO  @ Sun, 29 Jan 2017 00:06:44:  12000000 
INFO  @ Sun, 29 Jan 2017 00:06:46:  13000000 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1 tag size is determined as 46 bps 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1 tag size = 46 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1  total tags in treatment: 12245963 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1  total tags in control: 13736812 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:06:47: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #2 Use 215 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:06:47: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:07:39: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:07:39: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:07:39: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:07:39: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:07:39: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:09:43: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:09:45: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:09:46: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:09:47: Done! 
INFO  @ Sun, 29 Jan 2017 00:09:50: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 215 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 00:09:50: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:09:50: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:09:51:  1000000 
INFO  @ Sun, 29 Jan 2017 00:09:53:  2000000 
INFO  @ Sun, 29 Jan 2017 00:09:54:  3000000 
INFO  @ Sun, 29 Jan 2017 00:09:56:  4000000 
INFO  @ Sun, 29 Jan 2017 00:09:57:  5000000 
INFO  @ Sun, 29 Jan 2017 00:09:59:  6000000 
INFO  @ Sun, 29 Jan 2017 00:10:00:  7000000 
INFO  @ Sun, 29 Jan 2017 00:10:02:  8000000 
INFO  @ Sun, 29 Jan 2017 00:10:03:  9000000 
INFO  @ Sun, 29 Jan 2017 00:10:05:  10000000 
INFO  @ Sun, 29 Jan 2017 00:10:06:  11000000 
INFO  @ Sun, 29 Jan 2017 00:10:08:  12000000 
INFO  @ Sun, 29 Jan 2017 00:10:09: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:10:10:  1000000 
INFO  @ Sun, 29 Jan 2017 00:10:12:  2000000 
INFO  @ Sun, 29 Jan 2017 00:10:13:  3000000 
INFO  @ Sun, 29 Jan 2017 00:10:14:  4000000 
INFO  @ Sun, 29 Jan 2017 00:10:16:  5000000 
INFO  @ Sun, 29 Jan 2017 00:10:17:  6000000 
INFO  @ Sun, 29 Jan 2017 00:10:19:  7000000 
INFO  @ Sun, 29 Jan 2017 00:10:20:  8000000 
INFO  @ Sun, 29 Jan 2017 00:10:21:  9000000 
INFO  @ Sun, 29 Jan 2017 00:10:23:  10000000 
INFO  @ Sun, 29 Jan 2017 00:10:24:  11000000 
INFO  @ Sun, 29 Jan 2017 00:10:26:  12000000 
INFO  @ Sun, 29 Jan 2017 00:10:27:  13000000 
INFO  @ Sun, 29 Jan 2017 00:10:28: #1 tag size is determined as 46 bps 
INFO  @ Sun, 29 Jan 2017 00:10:28: #1 tag size = 46 
INFO  @ Sun, 29 Jan 2017 00:10:28: #1  total tags in treatment: 12245963 
INFO  @ Sun, 29 Jan 2017 00:10:28: #1  total tags in control: 13736812 
INFO  @ Sun, 29 Jan 2017 00:10:28: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:10:28: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:10:28: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:10:28: #2 Use 215 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:10:28: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:10:28: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:10:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:11:28: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:12:52: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:12:54: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:12:55: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:12:56: Done!

Num	18
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27
Name	macs2 rep1-pr2
Thread	thread_Root
PID	35949

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

Start	2017-01-29 00:05:56
End	2017-01-29 00:12:45
Elapsed	00:06:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

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

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 215 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

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

   
--------------------Stdout--------------------
16316 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:06:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 00:06:08: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:06:08: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:06:10:  1000000 
INFO  @ Sun, 29 Jan 2017 00:06:11:  2000000 
INFO  @ Sun, 29 Jan 2017 00:06:13:  3000000 
INFO  @ Sun, 29 Jan 2017 00:06:14:  4000000 
INFO  @ Sun, 29 Jan 2017 00:06:16:  5000000 
INFO  @ Sun, 29 Jan 2017 00:06:17:  6000000 
INFO  @ Sun, 29 Jan 2017 00:06:19:  7000000 
INFO  @ Sun, 29 Jan 2017 00:06:20:  8000000 
INFO  @ Sun, 29 Jan 2017 00:06:22:  9000000 
INFO  @ Sun, 29 Jan 2017 00:06:23:  10000000 
INFO  @ Sun, 29 Jan 2017 00:06:25:  11000000 
INFO  @ Sun, 29 Jan 2017 00:06:27:  12000000 
INFO  @ Sun, 29 Jan 2017 00:06:28: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:06:29:  1000000 
INFO  @ Sun, 29 Jan 2017 00:06:31:  2000000 
INFO  @ Sun, 29 Jan 2017 00:06:32:  3000000 
INFO  @ Sun, 29 Jan 2017 00:06:33:  4000000 
INFO  @ Sun, 29 Jan 2017 00:06:35:  5000000 
INFO  @ Sun, 29 Jan 2017 00:06:36:  6000000 
INFO  @ Sun, 29 Jan 2017 00:06:37:  7000000 
INFO  @ Sun, 29 Jan 2017 00:06:39:  8000000 
INFO  @ Sun, 29 Jan 2017 00:06:40:  9000000 
INFO  @ Sun, 29 Jan 2017 00:06:42:  10000000 
INFO  @ Sun, 29 Jan 2017 00:06:43:  11000000 
INFO  @ Sun, 29 Jan 2017 00:06:44:  12000000 
INFO  @ Sun, 29 Jan 2017 00:06:46:  13000000 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1 tag size is determined as 45 bps 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1 tag size = 45 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1  total tags in treatment: 12245963 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1  total tags in control: 13736812 
INFO  @ Sun, 29 Jan 2017 00:06:47: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:06:47: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #2 Use 215 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:06:47: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:06:47: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:07:40: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:07:40: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:07:40: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:07:40: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:07:40: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:09:46: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:09:48: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:09:49: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:09:50: Done! 
INFO  @ Sun, 29 Jan 2017 00:09:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 215 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/align/ctl1/SRR393672.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 00:09:53: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:09:53: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:09:55:  1000000 
INFO  @ Sun, 29 Jan 2017 00:09:56:  2000000 
INFO  @ Sun, 29 Jan 2017 00:09:58:  3000000 
INFO  @ Sun, 29 Jan 2017 00:09:59:  4000000 
INFO  @ Sun, 29 Jan 2017 00:10:01:  5000000 
INFO  @ Sun, 29 Jan 2017 00:10:02:  6000000 
INFO  @ Sun, 29 Jan 2017 00:10:04:  7000000 
INFO  @ Sun, 29 Jan 2017 00:10:05:  8000000 
INFO  @ Sun, 29 Jan 2017 00:10:07:  9000000 
INFO  @ Sun, 29 Jan 2017 00:10:08:  10000000 
INFO  @ Sun, 29 Jan 2017 00:10:10:  11000000 
INFO  @ Sun, 29 Jan 2017 00:10:11:  12000000 
INFO  @ Sun, 29 Jan 2017 00:10:13: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:10:14:  1000000 
INFO  @ Sun, 29 Jan 2017 00:10:15:  2000000 
INFO  @ Sun, 29 Jan 2017 00:10:17:  3000000 
INFO  @ Sun, 29 Jan 2017 00:10:18:  4000000 
INFO  @ Sun, 29 Jan 2017 00:10:19:  5000000 
INFO  @ Sun, 29 Jan 2017 00:10:21:  6000000 
INFO  @ Sun, 29 Jan 2017 00:10:22:  7000000 
INFO  @ Sun, 29 Jan 2017 00:10:24:  8000000 
INFO  @ Sun, 29 Jan 2017 00:10:25:  9000000 
INFO  @ Sun, 29 Jan 2017 00:10:27:  10000000 
INFO  @ Sun, 29 Jan 2017 00:10:28:  11000000 
INFO  @ Sun, 29 Jan 2017 00:10:29:  12000000 
INFO  @ Sun, 29 Jan 2017 00:10:31:  13000000 
INFO  @ Sun, 29 Jan 2017 00:10:32: #1 tag size is determined as 45 bps 
INFO  @ Sun, 29 Jan 2017 00:10:32: #1 tag size = 45 
INFO  @ Sun, 29 Jan 2017 00:10:32: #1  total tags in treatment: 12245963 
INFO  @ Sun, 29 Jan 2017 00:10:32: #1  total tags in control: 13736812 
INFO  @ Sun, 29 Jan 2017 00:10:32: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:10:32: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:10:32: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:10:32: #2 Use 215 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:10:32: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:10:32: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:10:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:11:24: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:12:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:12:37: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:12:38: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:12:39: Done!

Num	19
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28
Name	naive_overlap_thresh
Thread	thread_Root
PID	35993

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

Start	2017-01-29 00:35:47
End	2017-01-29 00:37:06
Elapsed	00:01:19
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 61

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

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 76

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

   
--------------------Stdout--------------------
7703 (process ID) old priority 0, new priority 10
Waiting for 55 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000214.1	131570	131883	Peak_3553	164	.	6.35146	16.42763	12.61741	203

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000214.1	131570	131883	Peak_3553	164	.	6.35146	16.42763	12.61741	203

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000214.1	131576	131883	Peak_1701	192	.	7.00850	19.24999	15.04461	201

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000214.1	131576	131883	Peak_1701	192	.	7.00850	19.24999	15.04461	201

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2	1251	1750	Peak_35738	68	.	4.84527	6.89599	4.36817	184

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2	1251	1750	Peak_35738	68	.	4.84527	6.89599	4.36817	184

Num	20
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29
Name	naive_overlap_thresh
Thread	thread_Root
PID	35994

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

Start	2017-01-29 00:35:48
End	2017-01-29 00:37:06
Elapsed	00:01:18
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Dependencies

 
# SYS command. line 61

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

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.gappedPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.gappedPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 76

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

   
--------------------Stdout--------------------
7701 (process ID) old priority 0, new priority 10
Waiting for 48 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000224.1	21396	21725	Peak_4323	35	.	21396	21725	0	2	1,1	0,328	3.43303	5.67598	3.59635

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000224.1	21396	21725	Peak_4323	35	.	21396	21725	0	2	1,1	0,328	3.43303	5.67598	3.59635

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	2209043	2209258	Peak_8076	26	.	2209043	2209258	0	2	1,1	0,214	3.76776	4.65653	2.65738

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	2209043	2209258	Peak_8076	26	.	2209043	2209258	0	2	1,1	0,214	3.76776	4.65653	2.65738

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000205.2	16394	22031	Peak_93285	4	.	16394	22031	0	2	1,1	0,5636	1.33445	1.31505	0.47194

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000205.2	16394	22031	Peak_93285	4	.	16394	22031	0	2	1,1	0,5636	1.33445	1.31505	0.47194

Num	21
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30
Name	naive_overlap_thresh
Thread	thread_Root
PID	35995

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

Start	2017-01-29 00:35:49
End	2017-01-29 00:37:07
Elapsed	00:01:18
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
Dependencies

 
# SYS command. line 61

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

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR393682.nodup.pr1.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR393682.nodup.pr2.tagAlign_x_SRR393672.nodup.tagAlign.broadPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.broadPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 76

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

   
--------------------Stdout--------------------
7702 (process ID) old priority 0, new priority 10
Waiting for 52 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000224.1	21396	21725	Peak_4323	35	.	3.43303	5.67598	3.59635

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000224.1	21396	21725	Peak_4323	35	.	3.43303	5.67598	3.59635

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	2209043	2209258	Peak_8076	26	.	3.76776	4.65653	2.65738

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	2209043	2209258	Peak_8076	26	.	3.76776	4.65653	2.65738

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000205.2	16394	22031	Peak_93285	4	.	1.33445	1.31505	0.47194

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000205.2	16394	22031	Peak_93285	4	.	1.33445	1.31505	0.47194

Num	22
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31
Name	blacklist_filter peak 1
Thread	thread_Root
PID	12098

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

Start	2017-01-29 00:37:09
End	2017-01-29 00:38:17
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

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

# SYS command. line 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

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

   
--------------------Stdout--------------------
12103 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000214.1	131575	131883	Peak_991	196	.	6.81828	19.68479	15.35321	201

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/rep1/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000214.1	131575	131883	Peak_991	196	.	6.81828	19.68479	15.35321	201

Num	23
ID	task.report.peak2hammock.line_412.id_32
Name	peak2hammock
Thread	thread_Root
PID	16302

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

Start	2017-01-29 00:38:18
End	2017-01-29 00:38:29
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 414

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

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
16306 (process ID) old priority 0, new priority 10

Num	24
ID	task.report.peak2hammock.line_412.id_33
Name	peak2hammock
Thread	thread_Root
PID	17036

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

Start	2017-01-29 00:38:30
End	2017-01-29 00:38:45
Elapsed	00:00:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock.gz
Dependencies

 
# SYS command. line 414

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

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/peak/macs2/overlap/SRR393682.nodup.tagAlign_x_SRR393672.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
17040 (process ID) old priority 0, new priority 10

Num	25
ID	task.graphviz.report.line_97.id_34
Name	report
Thread	thread_Root
PID	18007

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

Start	2017-01-29 00:38:46
End	2017-01-29 00:38:54
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

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

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/report/H2AK119Ub1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/report/H2AK119Ub1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/report/H2AK119Ub1_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
18013 (process ID) old priority 0, new priority 10

Num	26
ID	task.report.pdf2png.line_379.id_39
Name	pdf2png
Thread	thread_Root
PID	18012

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

Start	2017-01-29 00:38:46
End	2017-01-29 00:38:54
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.plot.png
Dependencies

 
# SYS command. line 380

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

# SYS command. line 381

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1/out/qc/rep1/SRR393682.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
18024 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, H2AK119Ub1, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393682.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/RawReadsFiles/SRR393672.fastq.gz, -final_stage, idr, -histone, $]
bool	canFail	false
string	CPATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_mOv3iE
string	LANG	en_US.UTF-8
string	LIBRARY_PATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Gao2012Data/H2AK119Ub1
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 32974 22
string	SSH_CONNECTION	171.65.77.8 32974 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	51044.H2AK119Ub1.BDS
string	system	sge
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int	timeout	-1
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	45170
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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Parallel (threads) details

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Global scope