Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170128_230014_090
Start time	2017-01-28 23:00:14
Run time	01:53:50.584
Tasks executed	26
Tasks failed	0
Tasks failed names
Arguments*	[-title, H3K4me2, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz, -final_stage, idr, -histone, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170128_230014_090/task.callpeak_macs2.macs2_rep1.line_71.id_25 chipseq.bds.20170128_230014_090/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26 chipseq.bds.20170128_230014_090/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27 chipseq.bds.20170128_230014_090/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28 chipseq.bds.20170128_230014_090/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29 chipseq.bds.20170128_230014_090/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30 chipseq.bds.20170128_230014_090/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31 chipseq.bds.20170128_230014_090/task.report.peak2hammock.line_412.id_32 chipseq.bds.20170128_230014_090/task.report.peak2hammock.line_412.id_33 chipseq.bds.20170128_230014_090/task.graphviz.report.line_97.id_34 chipseq.bds.20170128_230014_090/task.report.pdf2png.line_379.id_39
thread_42	thread_Root	chipseq.bds.20170128_230014_090_parallel_42/task.align_bwa.bwa_aln_ctl1.line_111.id_10 chipseq.bds.20170128_230014_090_parallel_42/task.align_bwa.bwa_sam_ctl1.line_143.id_13 chipseq.bds.20170128_230014_090_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_17 chipseq.bds.20170128_230014_090_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_20 chipseq.bds.20170128_230014_090_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_23 chipseq.bds.20170128_230014_090_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_24
thread_41	thread_Root	chipseq.bds.20170128_230014_090_parallel_41/task.align_bwa.bwa_aln_rep1.line_111.id_11 chipseq.bds.20170128_230014_090_parallel_41/task.align_bwa.bwa_sam_rep1.line_143.id_12 chipseq.bds.20170128_230014_090_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_14 chipseq.bds.20170128_230014_090_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_15 chipseq.bds.20170128_230014_090_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_16 chipseq.bds.20170128_230014_090_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_18 chipseq.bds.20170128_230014_090_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_19 chipseq.bds.20170128_230014_090_parallel_41/task.postalign_bed.spr_rep1.line_255.id_21 chipseq.bds.20170128_230014_090_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_22

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bwa.bwa_aln_ctl1.line_111.id_10
Name	bwa_aln ctl1
Thread	thread_42
PID	35886

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

Start	2017-01-28 23:00:15
End	2017-01-28 23:59:53
Elapsed	00:59:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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--------------------
56432 (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] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17560427 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/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 3552.906 sec; CPU: 3548.700 sec

Num	2
ID	task.align_bwa.bwa_aln_rep1.line_111.id_11
Name	bwa_aln rep1
Thread	thread_41
PID	35887

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

Start	2017-01-28 23:00:15
End	2017-01-28 23:49:27
Elapsed	00:49:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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--------------------
56423 (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] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.69 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.42 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.79 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.79 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.85 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.48 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.03 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.09 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.21 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.30 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.03 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.22 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.32 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.43 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.88 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.08 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.82 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.03 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.05 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.99 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.37 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.16 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.31 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.94 sec
[bwa_aln_core] write to the disk... 0.12 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.69 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.85 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.18 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.02 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.10 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.38 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.50 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.97 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.25 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.02 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.05 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.78 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.48 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.14 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.04 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.06 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.58 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.18 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.55 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.22 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.71 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.61 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.91 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.82 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.92 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.45 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.93 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.85 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.45 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.08 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.56 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.17 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.70 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.45 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.46 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.00 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.21 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.23 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.21 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.93 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.51 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.00 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.69 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.17 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.78 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.64 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.23 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.30 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.47 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.81 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.92 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.23 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.06 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.59 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.93 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.73 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.78 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.91 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.85 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.50 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.13 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.08 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.05 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25643976 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/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz
[main] Real time: 2926.542 sec; CPU: 8392.068 sec

Num	3
ID	task.align_bwa.bwa_sam_rep1.line_143.id_12
Name	bwa_sam rep1
Thread	thread_41
PID	35919

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

Start	2017-01-28 23:49:28
End	2017-01-29 00:03:23
Elapsed	00:13:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.bam

# SYS command. line 152

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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--------------------
16928 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.43 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.37 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.82 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.12 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.9% 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... 0.34 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 2.2% 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... 0.43 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 2.0% 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... 0.35 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.9% 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... 0.37 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 2.0% 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... 0.56 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.0% 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... 0.39 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 2.4% 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... 0.35 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.60 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.04 sec
[bwa_aln_core] refine gapped alignments... 2.11 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.24 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.97 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.38 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.71 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.00 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.72 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.75 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.39 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.43 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.52 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.16 sec
[bwa_aln_core] refine gapped alignments... 2.58 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.07 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.50 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.0% 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... 0.32 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.62 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.59 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.97 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 25643976 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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz
[main] Real time: 685.389 sec; CPU: 647.540 sec

Num	4
ID	task.align_bwa.bwa_sam_ctl1.line_143.id_13
Name	bwa_sam ctl1
Thread	thread_42
PID	35937

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

Start	2017-01-28 23:59:55
End	2017-01-29 00:11:30
Elapsed	00:11:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.bam

# SYS command. line 152

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.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--------------------
52150 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.33 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.41 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.81 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.48 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.33 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.53 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.18 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.35 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.07 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.14 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.45 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.60 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.87 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.77 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.56 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.57 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.51 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.43 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.34 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.45 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.53 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.53 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 1.22 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.40 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.70 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% 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] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.61 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.40 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.73 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.36 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.25 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.33 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.44 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.52 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.21 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.33 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.28 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.52 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.45 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.29 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.50 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.68 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.10 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.26 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 17560427 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/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 430.594 sec; CPU: 377.916 sec

Num	5
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_14
Name	dedup_bam_1 rep1
Thread	thread_41
PID	35945

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

Start	2017-01-29 00:03:24
End	2017-01-29 00:05:59
Elapsed	00:02:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.bam | \
			    	sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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--------------------
7691 (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	35950

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

Start	2017-01-29 00:06:00
End	2017-01-29 00:09:49
Elapsed	00:03:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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--------------------
17536 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:06:21 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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
[Sun Jan 29 00:06:21 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	2017-01-29 00:06:21	MarkDuplicates	Start of doWork freeMemory: 254879576; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:06:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:06:21	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-29 00:06:21	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1016000.4116552'.  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	2017-01-29 00:06:25	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:93,345,588
INFO	2017-01-29 00:06:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:27	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    2s.  Last read position: chr1:229,409,427
INFO	2017-01-29 00:06:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:30	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    3s.  Last read position: chr2:121,705,221
INFO	2017-01-29 00:06:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:33	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    2s.  Last read position: chr3:36,731,195
INFO	2017-01-29 00:06:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:35	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    2s.  Last read position: chr3:192,241,102
INFO	2017-01-29 00:06:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:38	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    2s.  Last read position: chr4:176,066,932
INFO	2017-01-29 00:06:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:41	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    3s.  Last read position: chr5:154,486,577
INFO	2017-01-29 00:06:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:44	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    2s.  Last read position: chr6:116,617,097
INFO	2017-01-29 00:06:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:46	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    2s.  Last read position: chr7:70,630,534
INFO	2017-01-29 00:06:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:49	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    2s.  Last read position: chr8:102,339,963
INFO	2017-01-29 00:06:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:51	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    2s.  Last read position: chr10:7,818,935
INFO	2017-01-29 00:06:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:56	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    5s.  Last read position: chr11:11,841,592
INFO	2017-01-29 00:06:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:06:59	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    2s.  Last read position: chr12:28,831,080
INFO	2017-01-29 00:06:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:01	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    2s.  Last read position: chr13:57,629,651
INFO	2017-01-29 00:07:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:03	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    2s.  Last read position: chr15:26,990,202
INFO	2017-01-29 00:07:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:08	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    4s.  Last read position: chr16:50,478,776
INFO	2017-01-29 00:07:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:11	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    2s.  Last read position: chr17:65,366,794
INFO	2017-01-29 00:07:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:13	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    2s.  Last read position: chr19:35,030,865
INFO	2017-01-29 00:07:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:15	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    2s.  Last read position: chr21:41,778,457
INFO	2017-01-29 00:07:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:18	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chrX:129,067,840
INFO	2017-01-29 00:07:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:07:18	MarkDuplicates	Read 20162647 records. 0 pairs never matched.
INFO	2017-01-29 00:07:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2745401912; totalMemory: 4439146496; maxMemory: 11453595648
INFO	2017-01-29 00:07:21	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:07:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:07:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:07:23	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:07:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 4394847256; totalMemory: 7309099008; maxMemory: 11453595648
INFO	2017-01-29 00:07:25	MarkDuplicates	Marking 958653 records as duplicates.
INFO	2017-01-29 00:07:25	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:08:35	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:09s.  Time for last 10,000,000:   69s.  Last read position: chr8:102,339,963
INFO	2017-01-29 00:09:47	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:22s.  Time for last 10,000,000:   72s.  Last read position: chrX:129,067,840
INFO	2017-01-29 00:09:48	MarkDuplicates	Before output close freeMemory: 7645617144; totalMemory: 7707033600; maxMemory: 11453595648
INFO	2017-01-29 00:09:48	MarkDuplicates	After output close freeMemory: 7526602608; totalMemory: 7588020224; maxMemory: 11453595648
[Sun Jan 29 00:09:48 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.46 minutes.
Runtime.totalMemory()=7588020224

Num	7
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_16
Name	dedup_bam_2 rep1
Thread	thread_41
PID	35954

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

Start	2017-01-29 00:09:51
End	2017-01-29 00:14:22
Elapsed	00:04:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.bam

# SYS command. line 153

 sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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--------------------
30163 (process ID) old priority 0, new priority 10

Num	8
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_17
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	35955

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

Start	2017-01-29 00:11:31
End	2017-01-29 00:15:36
Elapsed	00:04:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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--------------------
6453 (process ID) old priority 0, new priority 10

Num	9
ID	task.postalign_bam.bam_to_tag_rep1.line_505.id_18
Name	bam_to_tag rep1
Thread	thread_41
PID	35962

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

Start	2017-01-29 00:14:24
End	2017-01-29 00:15:36
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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--------------------
6612 (process ID) old priority 0, new priority 10

Waiting for 12 seconds.

Num	10
ID	task.postalign_bed.subsample_tag_rep1.line_45.id_19
Name	subsample_tag rep1
Thread	thread_41
PID	35964

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

Start	2017-01-29 00:15:38
End	2017-01-29 00:16:52
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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--------------------
6703 (process ID) old priority 0, new priority 10
Waiting for 28 seconds.

Num	11
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_20
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	35965

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

Start	2017-01-29 00:15:38
End	2017-01-29 00:18:46
Elapsed	00:03:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.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--------------------
6702 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:15:51 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.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
[Sun Jan 29 00:15:51 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-29 00:15:51	MarkDuplicates	Start of doWork freeMemory: 254879680; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:15:51	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:15:51	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2017-01-29 00:16:03	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position: chr2:7,720,599
INFO	2017-01-29 00:16:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:07	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    4s.  Last read position: chr3:32,290,878
INFO	2017-01-29 00:16:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:13	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    6s.  Last read position: chr5:31,410,244
INFO	2017-01-29 00:16:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:18	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    4s.  Last read position: chr6:76,055,404
INFO	2017-01-29 00:16:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:27	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    8s.  Last read position: chr7:134,138,515
INFO	2017-01-29 00:16:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:32	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    5s.  Last read position: chr9:137,609,223
INFO	2017-01-29 00:16:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:37	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    4s.  Last read position: chr11:121,062,334
INFO	2017-01-29 00:16:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:43	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    5s.  Last read position: chr14:86,188,790
INFO	2017-01-29 00:16:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:50	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    7s.  Last read position: chr17:58,813,264
INFO	2017-01-29 00:16:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:53	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    2s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:16:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:57	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    3s.  Last read position: chrX:100,440,272
INFO	2017-01-29 00:16:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:16:57	MarkDuplicates	Read 11369002 records. 0 pairs never matched.
INFO	2017-01-29 00:17:02	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3396535712; totalMemory: 4542431232; maxMemory: 11453595648
INFO	2017-01-29 00:17:02	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:17:05	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:17:05	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:17:06	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:17:07	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1613901840; totalMemory: 4542431232; maxMemory: 11453595648
INFO	2017-01-29 00:17:07	MarkDuplicates	Marking 167589 records as duplicates.
INFO	2017-01-29 00:17:07	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:18:34	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:25s.  Time for last 10,000,000:   85s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:18:43	MarkDuplicates	Before output close freeMemory: 8127069728; totalMemory: 8207204352; maxMemory: 11453595648
INFO	2017-01-29 00:18:45	MarkDuplicates	After output close freeMemory: 8018540952; totalMemory: 8098676736; maxMemory: 11453595648
[Sun Jan 29 00:18:45 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.89 minutes.
Runtime.totalMemory()=8098676736

Num	12
ID	task.postalign_bed.spr_rep1.line_255.id_21
Name	spr rep1
Thread	thread_41
PID	35966

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

Start	2017-01-29 00:15:39
End	2017-01-29 00:16:51
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz | wc -l )

# SYS command. line 261

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

# SYS command. line 265

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.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--------------------
49253 (process ID) old priority 0, new priority 10
Waiting for 17 seconds.

Num	13
ID	task.postalign_bed.xcor_rep1.line_212.id_22
Name	xcor rep1
Thread	thread_41
PID	35967

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

Start	2017-01-29 00:16:53
End	2017-01-29 00:26:10
Elapsed	00:09:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.15M.tagAlign.gz -p=3 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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--------------------
53681 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.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/Liu2013Data/H3K4me2/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/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.15M.tagAlign.gz 
opened /tmp/35967.1.q/Rtmp2gBNDB/SRR1016000.nodup.15M.tagAlignd3db69acaa06
done. read 15000000 fragments
ChIP data read length 48 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.196658 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.282579283473619 
Top 3 estimates for fragment length 150 
Window half size 895 
Phantom peak location 50 
Phantom peak Correlation 0.276232 
Normalized Strand cross-correlation coefficient (NSC) 1.436907 
Relative Strand cross-correlation Coefficient (RSC) 1.079766 
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	35971

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

Start	2017-01-29 00:18:48
End	2017-01-29 00:22:01
Elapsed	00:03:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/qc/ctl1/ENCFF001HNC.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--------------------
6962 (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	35976

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

Start	2017-01-29 00:22:03
End	2017-01-29 00:23:22
Elapsed	00:01:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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--------------------
7154 (process ID) old priority 0, new priority 10

Waiting for 35 seconds.

Num	16
ID	task.callpeak_macs2.macs2_rep1.line_71.id_25
Name	macs2 rep1
Thread	thread_Root
PID	35983

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

Start	2017-01-29 00:26:11
End	2017-01-29 00:51:06
Elapsed	00:24:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/signal/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/signal/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1 -o "SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/signal/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1 -o "SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/signal/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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--------------------
7418 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:26:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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 00:26:23: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:26:23: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:26:25:  1000000 
INFO  @ Sun, 29 Jan 2017 00:26:26:  2000000 
INFO  @ Sun, 29 Jan 2017 00:26:27:  3000000 
INFO  @ Sun, 29 Jan 2017 00:26:29:  4000000 
INFO  @ Sun, 29 Jan 2017 00:26:30:  5000000 
INFO  @ Sun, 29 Jan 2017 00:26:31:  6000000 
INFO  @ Sun, 29 Jan 2017 00:26:33:  7000000 
INFO  @ Sun, 29 Jan 2017 00:26:34:  8000000 
INFO  @ Sun, 29 Jan 2017 00:26:35:  9000000 
INFO  @ Sun, 29 Jan 2017 00:26:37:  10000000 
INFO  @ Sun, 29 Jan 2017 00:26:38:  11000000 
INFO  @ Sun, 29 Jan 2017 00:26:39:  12000000 
INFO  @ Sun, 29 Jan 2017 00:26:41:  13000000 
INFO  @ Sun, 29 Jan 2017 00:26:42:  14000000 
INFO  @ Sun, 29 Jan 2017 00:26:43:  15000000 
INFO  @ Sun, 29 Jan 2017 00:26:45:  16000000 
INFO  @ Sun, 29 Jan 2017 00:26:46:  17000000 
INFO  @ Sun, 29 Jan 2017 00:26:48:  18000000 
INFO  @ Sun, 29 Jan 2017 00:26:49:  19000000 
INFO  @ Sun, 29 Jan 2017 00:26:50: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:26:52:  1000000 
INFO  @ Sun, 29 Jan 2017 00:26:54:  2000000 
INFO  @ Sun, 29 Jan 2017 00:26:55:  3000000 
INFO  @ Sun, 29 Jan 2017 00:26:57:  4000000 
INFO  @ Sun, 29 Jan 2017 00:26:58:  5000000 
INFO  @ Sun, 29 Jan 2017 00:27:00:  6000000 
INFO  @ Sun, 29 Jan 2017 00:27:01:  7000000 
INFO  @ Sun, 29 Jan 2017 00:27:02:  8000000 
INFO  @ Sun, 29 Jan 2017 00:27:04:  9000000 
INFO  @ Sun, 29 Jan 2017 00:27:05:  10000000 
INFO  @ Sun, 29 Jan 2017 00:27:06:  11000000 
INFO  @ Sun, 29 Jan 2017 00:27:07: #1 tag size is determined as 46 bps 
INFO  @ Sun, 29 Jan 2017 00:27:07: #1 tag size = 46 
INFO  @ Sun, 29 Jan 2017 00:27:07: #1  total tags in treatment: 19203994 
INFO  @ Sun, 29 Jan 2017 00:27:07: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:27:07: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:27:07: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:27:07: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:27:07: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:27:07: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:27:07: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:27:07: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:28:03: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:28:03: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:28:03: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:28:03: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:28:03: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:30:17: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:30:18: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:30:18: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:30:19: Done! 
INFO  @ Sun, 29 Jan 2017 00:30:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/rep1/SRR1016000.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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 00:30:21: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:30:21: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:30:23:  1000000 
INFO  @ Sun, 29 Jan 2017 00:30:25:  2000000 
INFO  @ Sun, 29 Jan 2017 00:30:26:  3000000 
INFO  @ Sun, 29 Jan 2017 00:30:28:  4000000 
INFO  @ Sun, 29 Jan 2017 00:30:29:  5000000 
INFO  @ Sun, 29 Jan 2017 00:30:31:  6000000 
INFO  @ Sun, 29 Jan 2017 00:30:32:  7000000 
INFO  @ Sun, 29 Jan 2017 00:30:34:  8000000 
INFO  @ Sun, 29 Jan 2017 00:30:35:  9000000 
INFO  @ Sun, 29 Jan 2017 00:30:37:  10000000 
INFO  @ Sun, 29 Jan 2017 00:30:38:  11000000 
INFO  @ Sun, 29 Jan 2017 00:30:40:  12000000 
INFO  @ Sun, 29 Jan 2017 00:30:41:  13000000 
INFO  @ Sun, 29 Jan 2017 00:30:43:  14000000 
INFO  @ Sun, 29 Jan 2017 00:30:44:  15000000 
INFO  @ Sun, 29 Jan 2017 00:30:46:  16000000 
INFO  @ Sun, 29 Jan 2017 00:30:47:  17000000 
INFO  @ Sun, 29 Jan 2017 00:30:49:  18000000 
INFO  @ Sun, 29 Jan 2017 00:30:50:  19000000 
INFO  @ Sun, 29 Jan 2017 00:30:51: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:30:52:  1000000 
INFO  @ Sun, 29 Jan 2017 00:30:54:  2000000 
INFO  @ Sun, 29 Jan 2017 00:30:55:  3000000 
INFO  @ Sun, 29 Jan 2017 00:30:57:  4000000 
INFO  @ Sun, 29 Jan 2017 00:30:58:  5000000 
INFO  @ Sun, 29 Jan 2017 00:31:00:  6000000 
INFO  @ Sun, 29 Jan 2017 00:31:01:  7000000 
INFO  @ Sun, 29 Jan 2017 00:31:03:  8000000 
INFO  @ Sun, 29 Jan 2017 00:31:04:  9000000 
INFO  @ Sun, 29 Jan 2017 00:31:06:  10000000 
INFO  @ Sun, 29 Jan 2017 00:31:07:  11000000 
INFO  @ Sun, 29 Jan 2017 00:31:08: #1 tag size is determined as 46 bps 
INFO  @ Sun, 29 Jan 2017 00:31:08: #1 tag size = 46 
INFO  @ Sun, 29 Jan 2017 00:31:08: #1  total tags in treatment: 19203994 
INFO  @ Sun, 29 Jan 2017 00:31:08: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:31:08: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:31:08: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:31:08: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:31:08: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:31:08: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:31:08: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:31:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:31:59: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:32:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:32:56: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:32:57: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:32:58: Done! 
INFO  @ Sun, 29 Jan 2017 00:33:02: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:33:39: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:34:11: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 00:34:34: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 29 Jan 2017 00:37:03: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 00:38:34: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Sun, 29 Jan 2017 00:42:17: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:42:56: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 00:43:31: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 00:43:55: Values in your input bedGraph files will be multiplied by 11.201413 ... 
INFO  @ Sun, 29 Jan 2017 00:46:22: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Sun, 29 Jan 2017 00:46:39: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 00:47:45: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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	35984

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

Start	2017-01-29 00:26:12
End	2017-01-29 00:31:34
Elapsed	00:05:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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--------------------
30222 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:26:22: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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 00:26:22: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:26:22: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:26:24:  1000000 
INFO  @ Sun, 29 Jan 2017 00:26:25:  2000000 
INFO  @ Sun, 29 Jan 2017 00:26:27:  3000000 
INFO  @ Sun, 29 Jan 2017 00:26:28:  4000000 
INFO  @ Sun, 29 Jan 2017 00:26:30:  5000000 
INFO  @ Sun, 29 Jan 2017 00:26:31:  6000000 
INFO  @ Sun, 29 Jan 2017 00:26:33:  7000000 
INFO  @ Sun, 29 Jan 2017 00:26:35:  8000000 
INFO  @ Sun, 29 Jan 2017 00:26:36:  9000000 
INFO  @ Sun, 29 Jan 2017 00:26:38: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:26:39:  1000000 
INFO  @ Sun, 29 Jan 2017 00:26:40:  2000000 
INFO  @ Sun, 29 Jan 2017 00:26:42:  3000000 
INFO  @ Sun, 29 Jan 2017 00:26:43:  4000000 
INFO  @ Sun, 29 Jan 2017 00:26:44:  5000000 
INFO  @ Sun, 29 Jan 2017 00:26:46:  6000000 
INFO  @ Sun, 29 Jan 2017 00:26:47:  7000000 
INFO  @ Sun, 29 Jan 2017 00:26:49:  8000000 
INFO  @ Sun, 29 Jan 2017 00:26:50:  9000000 
INFO  @ Sun, 29 Jan 2017 00:26:51:  10000000 
INFO  @ Sun, 29 Jan 2017 00:26:53:  11000000 
INFO  @ Sun, 29 Jan 2017 00:26:53: #1 tag size is determined as 48 bps 
INFO  @ Sun, 29 Jan 2017 00:26:53: #1 tag size = 48 
INFO  @ Sun, 29 Jan 2017 00:26:53: #1  total tags in treatment: 9601997 
INFO  @ Sun, 29 Jan 2017 00:26:53: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:26:53: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:26:53: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:26:53: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:26:53: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:26:53: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:26:53: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:26:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:27:37: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:27:37: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:27:37: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:27:37: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:27:37: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:29:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:29:20: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:29:20: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:29:21: Done! 
INFO  @ Sun, 29 Jan 2017 00:29:24: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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 00:29:24: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:29:24: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:29:26:  1000000 
INFO  @ Sun, 29 Jan 2017 00:29:27:  2000000 
INFO  @ Sun, 29 Jan 2017 00:29:29:  3000000 
INFO  @ Sun, 29 Jan 2017 00:29:30:  4000000 
INFO  @ Sun, 29 Jan 2017 00:29:32:  5000000 
INFO  @ Sun, 29 Jan 2017 00:29:33:  6000000 
INFO  @ Sun, 29 Jan 2017 00:29:35:  7000000 
INFO  @ Sun, 29 Jan 2017 00:29:36:  8000000 
INFO  @ Sun, 29 Jan 2017 00:29:38:  9000000 
INFO  @ Sun, 29 Jan 2017 00:29:39: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:29:41:  1000000 
INFO  @ Sun, 29 Jan 2017 00:29:42:  2000000 
INFO  @ Sun, 29 Jan 2017 00:29:44:  3000000 
INFO  @ Sun, 29 Jan 2017 00:29:45:  4000000 
INFO  @ Sun, 29 Jan 2017 00:29:46:  5000000 
INFO  @ Sun, 29 Jan 2017 00:29:48:  6000000 
INFO  @ Sun, 29 Jan 2017 00:29:49:  7000000 
INFO  @ Sun, 29 Jan 2017 00:29:51:  8000000 
INFO  @ Sun, 29 Jan 2017 00:29:52:  9000000 
INFO  @ Sun, 29 Jan 2017 00:29:54:  10000000 
INFO  @ Sun, 29 Jan 2017 00:29:55:  11000000 
INFO  @ Sun, 29 Jan 2017 00:29:56: #1 tag size is determined as 48 bps 
INFO  @ Sun, 29 Jan 2017 00:29:56: #1 tag size = 48 
INFO  @ Sun, 29 Jan 2017 00:29:56: #1  total tags in treatment: 9601997 
INFO  @ Sun, 29 Jan 2017 00:29:56: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:29:56: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:29:56: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:29:56: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:29:56: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:29:56: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:29:56: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:29:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:30:37: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:31:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:31:26: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:31:27: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:31:28: Done!

Num	18
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27
Name	macs2 rep1-pr2
Thread	thread_Root
PID	35985

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

Start	2017-01-29 00:26:13
End	2017-01-29 00:31:55
Elapsed	00:05:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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--------------------
31419 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 00:26:37: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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 00:26:37: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:26:37: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:26:39:  1000000 
INFO  @ Sun, 29 Jan 2017 00:26:40:  2000000 
INFO  @ Sun, 29 Jan 2017 00:26:42:  3000000 
INFO  @ Sun, 29 Jan 2017 00:26:44:  4000000 
INFO  @ Sun, 29 Jan 2017 00:26:45:  5000000 
INFO  @ Sun, 29 Jan 2017 00:26:47:  6000000 
INFO  @ Sun, 29 Jan 2017 00:26:48:  7000000 
INFO  @ Sun, 29 Jan 2017 00:26:50:  8000000 
INFO  @ Sun, 29 Jan 2017 00:26:51:  9000000 
INFO  @ Sun, 29 Jan 2017 00:26:53: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:26:54:  1000000 
INFO  @ Sun, 29 Jan 2017 00:26:56:  2000000 
INFO  @ Sun, 29 Jan 2017 00:26:57:  3000000 
INFO  @ Sun, 29 Jan 2017 00:26:58:  4000000 
INFO  @ Sun, 29 Jan 2017 00:27:00:  5000000 
INFO  @ Sun, 29 Jan 2017 00:27:01:  6000000 
INFO  @ Sun, 29 Jan 2017 00:27:03:  7000000 
INFO  @ Sun, 29 Jan 2017 00:27:04:  8000000 
INFO  @ Sun, 29 Jan 2017 00:27:06:  9000000 
INFO  @ Sun, 29 Jan 2017 00:27:07:  10000000 
INFO  @ Sun, 29 Jan 2017 00:27:09:  11000000 
INFO  @ Sun, 29 Jan 2017 00:27:09: #1 tag size is determined as 47 bps 
INFO  @ Sun, 29 Jan 2017 00:27:09: #1 tag size = 47 
INFO  @ Sun, 29 Jan 2017 00:27:09: #1  total tags in treatment: 9601997 
INFO  @ Sun, 29 Jan 2017 00:27:09: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:27:09: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:27:09: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:27:09: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:27:09: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:27:09: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:27:09: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 00:27:09: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:27:55: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 00:27:55: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 00:27:55: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 00:27:55: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 00:27:55: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:29:39: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:29:39: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 00:29:40: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 00:29:40: Done! 
INFO  @ Sun, 29 Jan 2017 00:29:43: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/align/ctl1/ENCFF001HNC.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 00:29:43: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 00:29:43: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 00:29:44:  1000000 
INFO  @ Sun, 29 Jan 2017 00:29:46:  2000000 
INFO  @ Sun, 29 Jan 2017 00:29:47:  3000000 
INFO  @ Sun, 29 Jan 2017 00:29:49:  4000000 
INFO  @ Sun, 29 Jan 2017 00:29:50:  5000000 
INFO  @ Sun, 29 Jan 2017 00:29:52:  6000000 
INFO  @ Sun, 29 Jan 2017 00:29:54:  7000000 
INFO  @ Sun, 29 Jan 2017 00:29:55:  8000000 
INFO  @ Sun, 29 Jan 2017 00:29:57:  9000000 
INFO  @ Sun, 29 Jan 2017 00:29:58: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 00:30:00:  1000000 
INFO  @ Sun, 29 Jan 2017 00:30:01:  2000000 
INFO  @ Sun, 29 Jan 2017 00:30:02:  3000000 
INFO  @ Sun, 29 Jan 2017 00:30:04:  4000000 
INFO  @ Sun, 29 Jan 2017 00:30:05:  5000000 
INFO  @ Sun, 29 Jan 2017 00:30:07:  6000000 
INFO  @ Sun, 29 Jan 2017 00:30:08:  7000000 
INFO  @ Sun, 29 Jan 2017 00:30:09:  8000000 
INFO  @ Sun, 29 Jan 2017 00:30:11:  9000000 
INFO  @ Sun, 29 Jan 2017 00:30:12:  10000000 
INFO  @ Sun, 29 Jan 2017 00:30:14:  11000000 
INFO  @ Sun, 29 Jan 2017 00:30:14: #1 tag size is determined as 47 bps 
INFO  @ Sun, 29 Jan 2017 00:30:14: #1 tag size = 47 
INFO  @ Sun, 29 Jan 2017 00:30:14: #1  total tags in treatment: 9601997 
INFO  @ Sun, 29 Jan 2017 00:30:14: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 00:30:14: #1 finished! 
INFO  @ Sun, 29 Jan 2017 00:30:14: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 00:30:14: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 00:30:14: #2 Use 150 as fragment length 
INFO  @ Sun, 29 Jan 2017 00:30:14: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 00:30:14: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 00:30:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 00:30:57: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 00:31:45: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 00:31:47: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 00:31:48: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 00:31:49: Done!

Num	19
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28
Name	naive_overlap_thresh
Thread	thread_Root
PID	36024

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

Start	2017-01-29 00:51:07
End	2017-01-29 00:52:21
Elapsed	00:01:13
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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--------------------
6409 (process ID) old priority 0, new priority 10
Waiting for 58 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270772.1	90158	91649	Peak_44	1047	.	41.08398	104.71865	98.53228	345

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270772.1	90158	91649	Peak_44	1047	.	41.08398	104.71865	98.53228	345

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1	90103	91667	Peak_133	903	.	36.51910	90.36246	84.96340	479

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1	90103	91667	Peak_133	903	.	36.51910	90.36246	84.96340	479

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1	68200	68873	Peak_29031	61	.	3.89553	6.17367	4.05686	380

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1	68200	68873	Peak_29031	61	.	3.89553	6.17367	4.05686	380

Num	20
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29
Name	naive_overlap_thresh
Thread	thread_Root
PID	36025

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

Start	2017-01-29 00:51:09
End	2017-01-29 00:52:21
Elapsed	00:01:12
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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--------------------
6414 (process ID) old priority 0, new priority 10
Waiting for 54 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270819.1	85724	86328	Peak_6833	252	.	85724	86328	0	2	1,1	0,603	13.87914	27.73551	25.20529

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270819.1	85724	86328	Peak_6833	252	.	85724	86328	0	2	1,1	0,603	13.87914	27.73551	25.20529

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1	90026	91680	Peak_7368	251	.	90026	91680	0	3	1,1548,1	0,77,1653	12.04791	27.26950	25.13243

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1	90026	91680	Peak_7368	251	.	90026	91680	0	3	1,1548,1	0,77,1653	12.04791	27.26950	25.13243

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1	30185	30618	Peak_65542	4	.	30185	30618	0	3	1,150,1	0,281,432	2.35849	2.05660	0.42414

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1	30185	30618	Peak_65542	4	.	30185	30618	0	3	1,150,1	0,281,432	2.35849	2.05660	0.42414

Num	21
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30
Name	naive_overlap_thresh
Thread	thread_Root
PID	36026

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

Start	2017-01-29 00:51:10
End	2017-01-29 00:52:22
Elapsed	00:01:12
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016000.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016000.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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--------------------
6410 (process ID) old priority 0, new priority 10
Waiting for 56 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270819.1	85724	86328	Peak_6833	252	.	13.87914	27.73551	25.20529

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270819.1	85724	86328	Peak_6833	252	.	13.87914	27.73551	25.20529

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1	90026	91680	Peak_7368	251	.	12.04791	27.26950	25.13243

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1	90026	91680	Peak_7368	251	.	12.04791	27.26950	25.13243

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1	30185	30618	Peak_65542	4	.	2.35849	2.05660	0.42414

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1	30185	30618	Peak_65542	4	.	2.35849	2.05660	0.42414

Num	22
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31
Name	blacklist_filter peak 1
Thread	thread_Root
PID	10722

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

Start	2017-01-29 00:52:24
End	2017-01-29 00:53:32
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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--------------------
10726 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KI270772.1	90147	91651	Peak_59	1045	.	40.52559	104.57245	98.85706	355

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/rep1/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KI270772.1	90147	91651	Peak_59	1045	.	40.52559	104.57245	98.85706	355

Num	23
ID	task.report.peak2hammock.line_412.id_32
Name	peak2hammock
Thread	thread_Root
PID	15273

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

Start	2017-01-29 00:53:33
End	2017-01-29 00:53:44
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
15277 (process ID) old priority 0, new priority 10

Num	24
ID	task.report.peak2hammock.line_412.id_33
Name	peak2hammock
Thread	thread_Root
PID	16011

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

Start	2017-01-29 00:53:45
End	2017-01-29 00:53:55
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/peak/macs2/overlap/SRR1016000.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
16015 (process ID) old priority 0, new priority 10

Num	25
ID	task.graphviz.report.line_97.id_34
Name	report
Thread	thread_Root
PID	16738

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

Start	2017-01-29 00:53:56
End	2017-01-29 00:54:04
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/Liu2013Data/H3K4me2/out/report/H3K4me2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/report/H3K4me2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/report/H3K4me2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
16745 (process ID) old priority 0, new priority 10

Num	26
ID	task.report.pdf2png.line_379.id_39
Name	pdf2png
Thread	thread_Root
PID	16744

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

Start	2017-01-29 00:53:56
End	2017-01-29 00:54:04
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.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/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H3K4me2/out/qc/rep1/SRR1016000.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
16758 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, H3K4me2, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016000.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.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/Liu2013Data/H3K4me2
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/Liu2013Data/H3K4me2
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	21523.H3K4me2.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

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope