Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170127_155645_181
Start time	2017-01-27 15:56:45
Run time	01:22:20.042
Tasks executed	26
Tasks failed	0
Tasks failed names
Arguments*	[-species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz, -final_stage, idr, -histone, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170127_155645_181/task.callpeak_macs2.macs2_rep1.line_71.id_25 chipseq.bds.20170127_155645_181/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26 chipseq.bds.20170127_155645_181/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27 chipseq.bds.20170127_155645_181/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28 chipseq.bds.20170127_155645_181/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29 chipseq.bds.20170127_155645_181/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30 chipseq.bds.20170127_155645_181/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31 chipseq.bds.20170127_155645_181/task.report.peak2hammock.line_412.id_32 chipseq.bds.20170127_155645_181/task.report.peak2hammock.line_412.id_33 chipseq.bds.20170127_155645_181/task.graphviz.report.line_97.id_34 chipseq.bds.20170127_155645_181/task.report.pdf2png.line_379.id_39
thread_42	thread_Root	chipseq.bds.20170127_155645_181_parallel_42/task.align_bwa.bwa_aln_ctl1.line_111.id_10 chipseq.bds.20170127_155645_181_parallel_42/task.align_bwa.bwa_sam_ctl1.line_143.id_13 chipseq.bds.20170127_155645_181_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_17 chipseq.bds.20170127_155645_181_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_19 chipseq.bds.20170127_155645_181_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_22 chipseq.bds.20170127_155645_181_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_24
thread_41	thread_Root	chipseq.bds.20170127_155645_181_parallel_41/task.align_bwa.bwa_aln_rep1.line_111.id_11 chipseq.bds.20170127_155645_181_parallel_41/task.align_bwa.bwa_sam_rep1.line_143.id_12 chipseq.bds.20170127_155645_181_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_14 chipseq.bds.20170127_155645_181_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_15 chipseq.bds.20170127_155645_181_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_16 chipseq.bds.20170127_155645_181_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_18 chipseq.bds.20170127_155645_181_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_20 chipseq.bds.20170127_155645_181_parallel_41/task.postalign_bed.spr_rep1.line_255.id_21 chipseq.bds.20170127_155645_181_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_23

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	35697

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 15:56:47
End	2017-01-27 16:15:36
Elapsed	00:18:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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--------------------
40589 (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] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9795918 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz
[main] Real time: 1102.980 sec; CPU: 2157.504 sec

Num	2
ID	task.align_bwa.bwa_aln_rep1.line_111.id_11
Name	bwa_aln rep1
Thread	thread_41
PID	35698

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 15:56:47
End	2017-01-27 16:12:03
Elapsed	00:15:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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--------------------
40590 (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] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.50 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.66 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9795918 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz
[main] Real time: 890.211 sec; CPU: 1733.796 sec

Num	3
ID	task.align_bwa.bwa_sam_rep1.line_143.id_12
Name	bwa_sam rep1
Thread	thread_41
PID	35699

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 16:12:05
End	2017-01-27 16:45:14
Elapsed	00:33:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.bam

# SYS command. line 152

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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--------------------
26535 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.82 sec
[bwa_aln_core] refine gapped alignments... 6.59 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.34 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.50 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.30 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.29 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.11 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.28 sec
[bwa_aln_core] refine gapped alignments... 4.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.44 sec
[bwa_aln_core] refine gapped alignments... 4.89 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.26 sec
[bwa_aln_core] refine gapped alignments... 5.30 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.41 sec
[bwa_aln_core] refine gapped alignments... 5.53 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.07 sec
[bwa_aln_core] refine gapped alignments... 6.14 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.35 sec
[bwa_aln_core] refine gapped alignments... 6.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.68 sec
[bwa_aln_core] refine gapped alignments... 6.94 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.03 sec
[bwa_aln_core] refine gapped alignments... 6.96 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.69 sec
[bwa_aln_core] refine gapped alignments... 6.98 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.29 sec
[bwa_aln_core] refine gapped alignments... 7.06 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.93 sec
[bwa_aln_core] refine gapped alignments... 6.92 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.69 sec
[bwa_aln_core] refine gapped alignments... 6.91 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.47 sec
[bwa_aln_core] refine gapped alignments... 5.79 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.43 sec
[bwa_aln_core] refine gapped alignments... 4.06 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.13 sec
[bwa_aln_core] refine gapped alignments... 5.02 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.59 sec
[bwa_aln_core] refine gapped alignments... 4.69 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.09 sec
[bwa_aln_core] refine gapped alignments... 5.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.01 sec
[bwa_aln_core] refine gapped alignments... 5.63 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.30 sec
[bwa_aln_core] refine gapped alignments... 4.59 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.67 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.94 sec
[bwa_aln_core] refine gapped alignments... 11.55 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.74 sec
[bwa_aln_core] refine gapped alignments... 6.58 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.99 sec
[bwa_aln_core] refine gapped alignments... 6.32 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.49 sec
[bwa_aln_core] refine gapped alignments... 6.84 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.35 sec
[bwa_aln_core] refine gapped alignments... 8.64 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.19 sec
[bwa_aln_core] refine gapped alignments... 17.88 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 124.78 sec
[bwa_aln_core] refine gapped alignments... 11.99 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.63 sec
[bwa_aln_core] refine gapped alignments... 6.08 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.40 sec
[bwa_aln_core] refine gapped alignments... 4.65 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.27 sec
[bwa_aln_core] refine gapped alignments... 6.91 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.77 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.73 sec
[bwa_aln_core] refine gapped alignments... 7.16 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.28 sec
[bwa_aln_core] refine gapped alignments... 5.73 sec
[bwa_aln_core] print alignments... 0.13 sec
[bwa_aln_core] 9795918 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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz
[main] Real time: 1865.186 sec; CPU: 1837.020 sec

Num	4
ID	task.align_bwa.bwa_sam_ctl1.line_143.id_13
Name	bwa_sam ctl1
Thread	thread_42
PID	35700

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 16:15:38
End	2017-01-27 16:50:51
Elapsed	00:35:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.bam

# SYS command. line 152

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.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--------------------
26621 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.72 sec
[bwa_aln_core] refine gapped alignments... 7.03 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.75 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.65 sec
[bwa_aln_core] refine gapped alignments... 7.01 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.83 sec
[bwa_aln_core] refine gapped alignments... 6.95 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.80 sec
[bwa_aln_core] refine gapped alignments... 6.98 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.64 sec
[bwa_aln_core] refine gapped alignments... 6.95 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.32 sec
[bwa_aln_core] refine gapped alignments... 6.89 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.82 sec
[bwa_aln_core] refine gapped alignments... 6.92 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.26 sec
[bwa_aln_core] refine gapped alignments... 6.86 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.59 sec
[bwa_aln_core] refine gapped alignments... 6.98 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.45 sec
[bwa_aln_core] refine gapped alignments... 6.97 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.42 sec
[bwa_aln_core] refine gapped alignments... 6.90 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.68 sec
[bwa_aln_core] refine gapped alignments... 7.06 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.71 sec
[bwa_aln_core] refine gapped alignments... 7.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.47 sec
[bwa_aln_core] refine gapped alignments... 8.74 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.71 sec
[bwa_aln_core] refine gapped alignments... 7.83 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.64 sec
[bwa_aln_core] refine gapped alignments... 9.33 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.79 sec
[bwa_aln_core] refine gapped alignments... 8.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.93 sec
[bwa_aln_core] refine gapped alignments... 9.46 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.16 sec
[bwa_aln_core] refine gapped alignments... 8.95 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.21 sec
[bwa_aln_core] refine gapped alignments... 8.72 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.83 sec
[bwa_aln_core] refine gapped alignments... 7.09 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.47 sec
[bwa_aln_core] refine gapped alignments... 8.91 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.48 sec
[bwa_aln_core] refine gapped alignments... 8.96 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.04 sec
[bwa_aln_core] refine gapped alignments... 7.00 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.81 sec
[bwa_aln_core] refine gapped alignments... 6.94 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.89 sec
[bwa_aln_core] refine gapped alignments... 7.15 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.86 sec
[bwa_aln_core] refine gapped alignments... 7.10 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.26 sec
[bwa_aln_core] refine gapped alignments... 6.84 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.68 sec
[bwa_aln_core] refine gapped alignments... 6.99 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.66 sec
[bwa_aln_core] refine gapped alignments... 7.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.27 sec
[bwa_aln_core] refine gapped alignments... 7.18 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.52 sec
[bwa_aln_core] refine gapped alignments... 6.88 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.75 sec
[bwa_aln_core] refine gapped alignments... 7.04 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.56 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.13 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.07 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.25 sec
[bwa_aln_core] refine gapped alignments... 4.75 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.43 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.14 sec
[bwa_aln_core] 9795918 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/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz
[main] Real time: 1992.618 sec; CPU: 1964.088 sec

Num	5
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_14
Name	dedup_bam_1 rep1
Thread	thread_41
PID	35770

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 16:45:15
End	2017-01-27 16:47:32
Elapsed	00:02:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.bam | \
			    	sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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--------------------
5522 (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	35774

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

Start	2017-01-27 16:47:33
End	2017-01-27 16:50:12
Elapsed	00:02:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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--------------------
27910 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Fri Jan 27 16:48:07 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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
[Fri Jan 27 16:48:07 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	2017-01-27 16:48:07	MarkDuplicates	Start of doWork freeMemory: 254879584; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-27 16:48:07	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-27 16:48:07	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-27 16:48:08	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR2532030.7029141'.  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	2017-01-27 16:48:13	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr2:55,418,902
INFO	2017-01-27 16:48:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:19	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    5s.  Last read position: chr3:150,758,515
INFO	2017-01-27 16:48:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:23	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    3s.  Last read position: chr5:129,044,747
INFO	2017-01-27 16:48:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:27	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    4s.  Last read position: chr7:104,553,760
INFO	2017-01-27 16:48:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:33	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    5s.  Last read position: chr10:71,964,337
INFO	2017-01-27 16:48:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:36	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    2s.  Last read position: chr13:45,215,780
INFO	2017-01-27 16:48:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:40	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    4s.  Last read position: chr17:16,378,686
INFO	2017-01-27 16:48:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:43	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    3s.  Last read position: chrX:97,225,322
INFO	2017-01-27 16:48:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:48:43	MarkDuplicates	Read 8165118 records. 0 pairs never matched.
INFO	2017-01-27 16:48:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1807567920; totalMemory: 2718433280; maxMemory: 11453595648
INFO	2017-01-27 16:48:46	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-27 16:49:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-27 16:49:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-27 16:49:05	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-27 16:49:06	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2682879952; totalMemory: 5582094336; maxMemory: 11453595648
INFO	2017-01-27 16:49:06	MarkDuplicates	Marking 370943 records as duplicates.
INFO	2017-01-27 16:49:06	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-27 16:50:09	MarkDuplicates	Before output close freeMemory: 6074273224; totalMemory: 6123159552; maxMemory: 11453595648
INFO	2017-01-27 16:50:10	MarkDuplicates	After output close freeMemory: 6135613760; totalMemory: 6184501248; maxMemory: 11453595648
[Fri Jan 27 16:50:10 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.06 minutes.
Runtime.totalMemory()=6184501248

Num	7
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_16
Name	dedup_bam_2 rep1
Thread	thread_41
PID	35779

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 16:50:13
End	2017-01-27 16:52:48
Elapsed	00:02:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.bam

# SYS command. line 153

 sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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--------------------
29933 (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	35780

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 16:50:53
End	2017-01-27 16:52:52
Elapsed	00:01:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.bam | \
			    	sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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--------------------
33297 (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	35782

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

Start	2017-01-27 16:52:49
End	2017-01-27 16:54:07
Elapsed	00:01:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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--------------------
28439 (process ID) old priority 0, new priority 10

Waiting for 42 seconds.

Num	10
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_19
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	35783

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

Start	2017-01-27 16:52:53
End	2017-01-27 16:55:03
Elapsed	00:02:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.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--------------------
28438 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Fri Jan 27 16:53:07 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.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
[Fri Jan 27 16:53:07 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	2017-01-27 16:53:07	MarkDuplicates	Start of doWork freeMemory: 254879728; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-27 16:53:07	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-27 16:53:07	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-27 16:53:07	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR2532031.7594466'.  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	2017-01-27 16:53:12	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr2:84,259,537
INFO	2017-01-27 16:53:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:53:16	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    4s.  Last read position: chr3:189,530,251
INFO	2017-01-27 16:53:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:53:21	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    5s.  Last read position: chr6:3,215,105
INFO	2017-01-27 16:53:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:53:25	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    3s.  Last read position: chr8:33,724,508
INFO	2017-01-27 16:53:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:53:28	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    3s.  Last read position: chr11:22,120,616
INFO	2017-01-27 16:53:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:53:33	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    4s.  Last read position: chr13:103,292,887
INFO	2017-01-27 16:53:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:53:36	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    2s.  Last read position: chr19:44,908,075
INFO	2017-01-27 16:53:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-27 16:53:39	MarkDuplicates	Read 7759676 records. 0 pairs never matched.
INFO	2017-01-27 16:53:41	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1609222328; totalMemory: 2489319424; maxMemory: 11453595648
INFO	2017-01-27 16:53:41	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-27 16:54:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-27 16:54:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-27 16:54:00	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-27 16:54:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2462256088; totalMemory: 5356650496; maxMemory: 11453595648
INFO	2017-01-27 16:54:02	MarkDuplicates	Marking 104979 records as duplicates.
INFO	2017-01-27 16:54:02	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-27 16:55:00	MarkDuplicates	Before output close freeMemory: 5639662344; totalMemory: 5679087616; maxMemory: 11453595648
INFO	2017-01-27 16:55:02	MarkDuplicates	After output close freeMemory: 5705197184; totalMemory: 5744623616; maxMemory: 11453595648
[Fri Jan 27 16:55:02 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.93 minutes.
Runtime.totalMemory()=5744623616

Num	11
ID	task.postalign_bed.subsample_tag_rep1.line_45.id_20
Name	subsample_tag rep1
Thread	thread_41
PID	35785

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

Start	2017-01-27 16:54:09
End	2017-01-27 16:55:22
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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--------------------
28698 (process ID) old priority 0, new priority 10
Waiting for 45 seconds.

Num	12
ID	task.postalign_bed.spr_rep1.line_255.id_21
Name	spr rep1
Thread	thread_41
PID	35786

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

Start	2017-01-27 16:54:09
End	2017-01-27 16:55:23
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz | wc -l )

# SYS command. line 261

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

# SYS command. line 265

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.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--------------------
28699 (process ID) old priority 0, new priority 10
Waiting for 39 seconds.

Num	13
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_22
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	35787

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 16:55:05
End	2017-01-27 16:57:21
Elapsed	00:02:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.bam

# SYS command. line 153

 sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/qc/ctl1/SRR2532031.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--------------------
55947 (process ID) old priority 0, new priority 10

Num	14
ID	task.postalign_bed.xcor_rep1.line_212.id_23
Name	xcor rep1
Thread	thread_41
PID	35788

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2017-01-27 16:55:24
End	2017-01-27 17:01:36
Elapsed	00:06:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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--------------------
728 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.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: 2 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/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/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.15M.tagAlign.gz 
opened /tmp/35788.1.q/RtmpURA8oC/SRR2532030.nodup.15M.tagAlign95d79e9988c
done. read 7792886 fragments
ChIP data read length 49 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.09973635 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.110809746195814,0.104580474718593,0.104543193996282 
Top 3 estimates for fragment length 150,285,320 
Window half size 415 
Phantom peak location 40 
Phantom peak Correlation 0.1065764 
Normalized Strand cross-correlation coefficient (NSC) 1.111027 
Relative Strand cross-correlation Coefficient (RSC) 1.618914 
Phantom Peak Quality Tag 2 
null device 
          1 

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

Num	15
ID	task.postalign_bam.bam_to_tag_ctl1.line_505.id_24
Name	bam_to_tag ctl1
Thread	thread_42
PID	35792

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

Start	2017-01-27 16:57:23
End	2017-01-27 16:58:37
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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--------------------
29055 (process ID) old priority 0, new priority 10

Waiting for 40 seconds.

Num	16
ID	task.callpeak_macs2.macs2_rep1.line_71.id_25
Name	macs2 rep1
Thread	thread_Root
PID	35796

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

Start	2017-01-27 17:01:38
End	2017-01-27 17:15:26
Elapsed	00:13:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/signal/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/signal/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1 -o "SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/signal/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1 -o "SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/signal/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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--------------------
29346 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 27 Jan 2017 17:01:54: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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  @ Fri, 27 Jan 2017 17:01:54: #1 read tag files... 
INFO  @ Fri, 27 Jan 2017 17:01:54: #1 read treatment tags... 
INFO  @ Fri, 27 Jan 2017 17:01:56:  1000000 
INFO  @ Fri, 27 Jan 2017 17:01:57:  2000000 
INFO  @ Fri, 27 Jan 2017 17:01:59:  3000000 
INFO  @ Fri, 27 Jan 2017 17:02:00:  4000000 
INFO  @ Fri, 27 Jan 2017 17:02:02:  5000000 
INFO  @ Fri, 27 Jan 2017 17:02:03:  6000000 
INFO  @ Fri, 27 Jan 2017 17:02:05:  7000000 
INFO  @ Fri, 27 Jan 2017 17:02:06: #1.2 read input tags... 
INFO  @ Fri, 27 Jan 2017 17:02:08:  1000000 
INFO  @ Fri, 27 Jan 2017 17:02:09:  2000000 
INFO  @ Fri, 27 Jan 2017 17:02:10:  3000000 
INFO  @ Fri, 27 Jan 2017 17:02:12:  4000000 
INFO  @ Fri, 27 Jan 2017 17:02:13:  5000000 
INFO  @ Fri, 27 Jan 2017 17:02:15:  6000000 
INFO  @ Fri, 27 Jan 2017 17:02:16:  7000000 
INFO  @ Fri, 27 Jan 2017 17:02:17: #1 tag size is determined as 49 bps 
INFO  @ Fri, 27 Jan 2017 17:02:17: #1 tag size = 49 
INFO  @ Fri, 27 Jan 2017 17:02:17: #1  total tags in treatment: 7794175 
INFO  @ Fri, 27 Jan 2017 17:02:17: #1  total tags in control: 7654697 
INFO  @ Fri, 27 Jan 2017 17:02:17: #1 finished! 
INFO  @ Fri, 27 Jan 2017 17:02:17: #2 Build Peak Model... 
INFO  @ Fri, 27 Jan 2017 17:02:17: #2 Skipped... 
INFO  @ Fri, 27 Jan 2017 17:02:17: #2 Use 150 as fragment length 
INFO  @ Fri, 27 Jan 2017 17:02:17: #3 Call peaks... 
INFO  @ Fri, 27 Jan 2017 17:02:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 27 Jan 2017 17:02:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 27 Jan 2017 17:02:47: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 27 Jan 2017 17:02:47: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 27 Jan 2017 17:02:47: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_control_lambda.bdg 
INFO  @ Fri, 27 Jan 2017 17:02:47: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 27 Jan 2017 17:02:47: #3 Call peaks for each chromosome... 
INFO  @ Fri, 27 Jan 2017 17:04:06: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.xls 
INFO  @ Fri, 27 Jan 2017 17:04:07: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 27 Jan 2017 17:04:08: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_summits.bed 
INFO  @ Fri, 27 Jan 2017 17:04:08: Done! 
INFO  @ Fri, 27 Jan 2017 17:04:10: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/rep1/SRR2532030.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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  @ Fri, 27 Jan 2017 17:04:10: #1 read tag files... 
INFO  @ Fri, 27 Jan 2017 17:04:10: #1 read treatment tags... 
INFO  @ Fri, 27 Jan 2017 17:04:12:  1000000 
INFO  @ Fri, 27 Jan 2017 17:04:14:  2000000 
INFO  @ Fri, 27 Jan 2017 17:04:15:  3000000 
INFO  @ Fri, 27 Jan 2017 17:04:17:  4000000 
INFO  @ Fri, 27 Jan 2017 17:04:18:  5000000 
INFO  @ Fri, 27 Jan 2017 17:04:20:  6000000 
INFO  @ Fri, 27 Jan 2017 17:04:21:  7000000 
INFO  @ Fri, 27 Jan 2017 17:04:23: #1.2 read input tags... 
INFO  @ Fri, 27 Jan 2017 17:04:24:  1000000 
INFO  @ Fri, 27 Jan 2017 17:04:26:  2000000 
INFO  @ Fri, 27 Jan 2017 17:04:27:  3000000 
INFO  @ Fri, 27 Jan 2017 17:04:29:  4000000 
INFO  @ Fri, 27 Jan 2017 17:04:30:  5000000 
INFO  @ Fri, 27 Jan 2017 17:04:32:  6000000 
INFO  @ Fri, 27 Jan 2017 17:04:33:  7000000 
INFO  @ Fri, 27 Jan 2017 17:04:35: #1 tag size is determined as 49 bps 
INFO  @ Fri, 27 Jan 2017 17:04:35: #1 tag size = 49 
INFO  @ Fri, 27 Jan 2017 17:04:35: #1  total tags in treatment: 7794175 
INFO  @ Fri, 27 Jan 2017 17:04:35: #1  total tags in control: 7654697 
INFO  @ Fri, 27 Jan 2017 17:04:35: #1 finished! 
INFO  @ Fri, 27 Jan 2017 17:04:35: #2 Build Peak Model... 
INFO  @ Fri, 27 Jan 2017 17:04:35: #2 Skipped... 
INFO  @ Fri, 27 Jan 2017 17:04:35: #2 Use 150 as fragment length 
INFO  @ Fri, 27 Jan 2017 17:04:35: #3 Call peaks... 
INFO  @ Fri, 27 Jan 2017 17:04:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 27 Jan 2017 17:04:35: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 27 Jan 2017 17:05:04: #3 Call peaks for each chromosome... 
INFO  @ Fri, 27 Jan 2017 17:05:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.xls 
INFO  @ Fri, 27 Jan 2017 17:05:30: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.broadPeak 
INFO  @ Fri, 27 Jan 2017 17:05:31: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 27 Jan 2017 17:05:33: Done! 
INFO  @ Fri, 27 Jan 2017 17:05:40: Read and build treatment bedGraph... 
INFO  @ Fri, 27 Jan 2017 17:05:55: Read and build control bedGraph... 
INFO  @ Fri, 27 Jan 2017 17:06:17: Build scoreTrackII... 
INFO  @ Fri, 27 Jan 2017 17:06:29: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 27 Jan 2017 17:07:53: Write bedGraph of scores... 
INFO  @ Fri, 27 Jan 2017 17:08:34: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign_FE.bdg'! 
INFO  @ Fri, 27 Jan 2017 17:10:16: Read and build treatment bedGraph... 
INFO  @ Fri, 27 Jan 2017 17:10:30: Read and build control bedGraph... 
INFO  @ Fri, 27 Jan 2017 17:10:52: Build scoreTrackII... 
INFO  @ Fri, 27 Jan 2017 17:11:04: Values in your input bedGraph files will be multiplied by 7.654697 ... 
INFO  @ Fri, 27 Jan 2017 17:12:26: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 27 Jan 2017 17:12:37: Write bedGraph of scores... 
INFO  @ Fri, 27 Jan 2017 17:13:18: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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	35797

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

Start	2017-01-27 17:01:39
End	2017-01-27 17:05:56
Elapsed	00:04:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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--------------------
29347 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 27 Jan 2017 17:01:54: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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  @ Fri, 27 Jan 2017 17:01:54: #1 read tag files... 
INFO  @ Fri, 27 Jan 2017 17:01:54: #1 read treatment tags... 
INFO  @ Fri, 27 Jan 2017 17:01:56:  1000000 
INFO  @ Fri, 27 Jan 2017 17:01:58:  2000000 
INFO  @ Fri, 27 Jan 2017 17:01:59:  3000000 
INFO  @ Fri, 27 Jan 2017 17:02:01: #1.2 read input tags... 
INFO  @ Fri, 27 Jan 2017 17:02:03:  1000000 
INFO  @ Fri, 27 Jan 2017 17:02:04:  2000000 
INFO  @ Fri, 27 Jan 2017 17:02:06:  3000000 
INFO  @ Fri, 27 Jan 2017 17:02:07:  4000000 
INFO  @ Fri, 27 Jan 2017 17:02:09:  5000000 
INFO  @ Fri, 27 Jan 2017 17:02:10:  6000000 
INFO  @ Fri, 27 Jan 2017 17:02:11:  7000000 
INFO  @ Fri, 27 Jan 2017 17:02:13: #1 tag size is determined as 49 bps 
INFO  @ Fri, 27 Jan 2017 17:02:13: #1 tag size = 49 
INFO  @ Fri, 27 Jan 2017 17:02:13: #1  total tags in treatment: 3897088 
INFO  @ Fri, 27 Jan 2017 17:02:13: #1  total tags in control: 7654697 
INFO  @ Fri, 27 Jan 2017 17:02:13: #1 finished! 
INFO  @ Fri, 27 Jan 2017 17:02:13: #2 Build Peak Model... 
INFO  @ Fri, 27 Jan 2017 17:02:13: #2 Skipped... 
INFO  @ Fri, 27 Jan 2017 17:02:13: #2 Use 150 as fragment length 
INFO  @ Fri, 27 Jan 2017 17:02:13: #3 Call peaks... 
INFO  @ Fri, 27 Jan 2017 17:02:13: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 27 Jan 2017 17:02:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 27 Jan 2017 17:02:38: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 27 Jan 2017 17:02:38: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 27 Jan 2017 17:02:38: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_control_lambda.bdg 
INFO  @ Fri, 27 Jan 2017 17:02:38: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 27 Jan 2017 17:02:38: #3 Call peaks for each chromosome... 
INFO  @ Fri, 27 Jan 2017 17:03:46: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.xls 
INFO  @ Fri, 27 Jan 2017 17:03:47: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 27 Jan 2017 17:03:48: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_summits.bed 
INFO  @ Fri, 27 Jan 2017 17:03:48: Done! 
INFO  @ Fri, 27 Jan 2017 17:03:52: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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  @ Fri, 27 Jan 2017 17:03:52: #1 read tag files... 
INFO  @ Fri, 27 Jan 2017 17:03:52: #1 read treatment tags... 
INFO  @ Fri, 27 Jan 2017 17:03:54:  1000000 
INFO  @ Fri, 27 Jan 2017 17:03:56:  2000000 
INFO  @ Fri, 27 Jan 2017 17:03:57:  3000000 
INFO  @ Fri, 27 Jan 2017 17:03:59: #1.2 read input tags... 
INFO  @ Fri, 27 Jan 2017 17:04:01:  1000000 
INFO  @ Fri, 27 Jan 2017 17:04:02:  2000000 
INFO  @ Fri, 27 Jan 2017 17:04:03:  3000000 
INFO  @ Fri, 27 Jan 2017 17:04:05:  4000000 
INFO  @ Fri, 27 Jan 2017 17:04:07:  5000000 
INFO  @ Fri, 27 Jan 2017 17:04:08:  6000000 
INFO  @ Fri, 27 Jan 2017 17:04:10:  7000000 
INFO  @ Fri, 27 Jan 2017 17:04:11: #1 tag size is determined as 49 bps 
INFO  @ Fri, 27 Jan 2017 17:04:11: #1 tag size = 49 
INFO  @ Fri, 27 Jan 2017 17:04:11: #1  total tags in treatment: 3897088 
INFO  @ Fri, 27 Jan 2017 17:04:11: #1  total tags in control: 7654697 
INFO  @ Fri, 27 Jan 2017 17:04:11: #1 finished! 
INFO  @ Fri, 27 Jan 2017 17:04:11: #2 Build Peak Model... 
INFO  @ Fri, 27 Jan 2017 17:04:11: #2 Skipped... 
INFO  @ Fri, 27 Jan 2017 17:04:11: #2 Use 150 as fragment length 
INFO  @ Fri, 27 Jan 2017 17:04:11: #3 Call peaks... 
INFO  @ Fri, 27 Jan 2017 17:04:11: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 27 Jan 2017 17:04:11: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 27 Jan 2017 17:04:36: #3 Call peaks for each chromosome... 
INFO  @ Fri, 27 Jan 2017 17:05:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.xls 
INFO  @ Fri, 27 Jan 2017 17:05:31: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.broadPeak 
INFO  @ Fri, 27 Jan 2017 17:05:36: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 27 Jan 2017 17:05:41: Done!

Num	18
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27
Name	macs2 rep1-pr2
Thread	thread_Root
PID	35798

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

Start	2017-01-27 17:01:41
End	2017-01-27 17:06:23
Elapsed	00:04:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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--------------------
27950 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 27 Jan 2017 17:02:06: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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  @ Fri, 27 Jan 2017 17:02:06: #1 read tag files... 
INFO  @ Fri, 27 Jan 2017 17:02:06: #1 read treatment tags... 
INFO  @ Fri, 27 Jan 2017 17:02:08:  1000000 
INFO  @ Fri, 27 Jan 2017 17:02:09:  2000000 
INFO  @ Fri, 27 Jan 2017 17:02:11:  3000000 
INFO  @ Fri, 27 Jan 2017 17:02:12: #1.2 read input tags... 
INFO  @ Fri, 27 Jan 2017 17:02:14:  1000000 
INFO  @ Fri, 27 Jan 2017 17:02:16:  2000000 
INFO  @ Fri, 27 Jan 2017 17:02:17:  3000000 
INFO  @ Fri, 27 Jan 2017 17:02:19:  4000000 
INFO  @ Fri, 27 Jan 2017 17:02:20:  5000000 
INFO  @ Fri, 27 Jan 2017 17:02:22:  6000000 
INFO  @ Fri, 27 Jan 2017 17:02:23:  7000000 
INFO  @ Fri, 27 Jan 2017 17:02:24: #1 tag size is determined as 47 bps 
INFO  @ Fri, 27 Jan 2017 17:02:24: #1 tag size = 47 
INFO  @ Fri, 27 Jan 2017 17:02:24: #1  total tags in treatment: 3897087 
INFO  @ Fri, 27 Jan 2017 17:02:24: #1  total tags in control: 7654697 
INFO  @ Fri, 27 Jan 2017 17:02:24: #1 finished! 
INFO  @ Fri, 27 Jan 2017 17:02:24: #2 Build Peak Model... 
INFO  @ Fri, 27 Jan 2017 17:02:24: #2 Skipped... 
INFO  @ Fri, 27 Jan 2017 17:02:24: #2 Use 150 as fragment length 
INFO  @ Fri, 27 Jan 2017 17:02:24: #3 Call peaks... 
INFO  @ Fri, 27 Jan 2017 17:02:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 27 Jan 2017 17:02:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 27 Jan 2017 17:02:55: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 27 Jan 2017 17:02:55: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 27 Jan 2017 17:02:55: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_control_lambda.bdg 
INFO  @ Fri, 27 Jan 2017 17:02:55: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 27 Jan 2017 17:02:55: #3 Call peaks for each chromosome... 
INFO  @ Fri, 27 Jan 2017 17:04:02: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.xls 
INFO  @ Fri, 27 Jan 2017 17:04:03: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 27 Jan 2017 17:04:03: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_summits.bed 
INFO  @ Fri, 27 Jan 2017 17:04:04: Done! 
INFO  @ Fri, 27 Jan 2017 17:04:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/align/ctl1/SRR2532031.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  @ Fri, 27 Jan 2017 17:04:08: #1 read tag files... 
INFO  @ Fri, 27 Jan 2017 17:04:08: #1 read treatment tags... 
INFO  @ Fri, 27 Jan 2017 17:04:09:  1000000 
INFO  @ Fri, 27 Jan 2017 17:04:11:  2000000 
INFO  @ Fri, 27 Jan 2017 17:04:13:  3000000 
INFO  @ Fri, 27 Jan 2017 17:04:14: #1.2 read input tags... 
INFO  @ Fri, 27 Jan 2017 17:04:16:  1000000 
INFO  @ Fri, 27 Jan 2017 17:04:17:  2000000 
INFO  @ Fri, 27 Jan 2017 17:04:19:  3000000 
INFO  @ Fri, 27 Jan 2017 17:04:20:  4000000 
INFO  @ Fri, 27 Jan 2017 17:04:22:  5000000 
INFO  @ Fri, 27 Jan 2017 17:04:23:  6000000 
INFO  @ Fri, 27 Jan 2017 17:04:25:  7000000 
INFO  @ Fri, 27 Jan 2017 17:04:26: #1 tag size is determined as 47 bps 
INFO  @ Fri, 27 Jan 2017 17:04:26: #1 tag size = 47 
INFO  @ Fri, 27 Jan 2017 17:04:26: #1  total tags in treatment: 3897087 
INFO  @ Fri, 27 Jan 2017 17:04:26: #1  total tags in control: 7654697 
INFO  @ Fri, 27 Jan 2017 17:04:26: #1 finished! 
INFO  @ Fri, 27 Jan 2017 17:04:26: #2 Build Peak Model... 
INFO  @ Fri, 27 Jan 2017 17:04:26: #2 Skipped... 
INFO  @ Fri, 27 Jan 2017 17:04:26: #2 Use 150 as fragment length 
INFO  @ Fri, 27 Jan 2017 17:04:26: #3 Call peaks... 
INFO  @ Fri, 27 Jan 2017 17:04:26: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 27 Jan 2017 17:04:26: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 27 Jan 2017 17:05:02: #3 Call peaks for each chromosome... 
INFO  @ Fri, 27 Jan 2017 17:05:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.xls 
INFO  @ Fri, 27 Jan 2017 17:06:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.broadPeak 
INFO  @ Fri, 27 Jan 2017 17:06:04: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 27 Jan 2017 17:06:08: Done!

Num	19
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28
Name	naive_overlap_thresh
Thread	thread_Root
PID	35811

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

Start	2017-01-27 17:15:28
End	2017-01-27 17:16:53
Elapsed	00:01:25
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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--------------------
30686 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2	140187	140337	Peak_26831	41	.	3.28811	4.11329	1.27103	22

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2	140187	140337	Peak_26831	41	.	3.28811	4.11329	1.27103	22

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL383557.1	54711	54863	Peak_16100	54	.	4.11014	5.47999	2.41770	49

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL383557.1	54711	54863	Peak_16100	54	.	4.11014	5.47999	2.41770	49

Num	20
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29
Name	naive_overlap_thresh
Thread	thread_Root
PID	35812

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

Start	2017-01-27 17:15:28
End	2017-01-27 17:16:52
Elapsed	00:01:24
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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--------------------
30685 (process ID) old priority 0, new priority 10
Waiting for 43 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270772.1	80077	80302	Peak_43315	5	.	80077	80302	0	3	1,150,1	0,4,224	2.15378	2.49792	0.51405

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270772.1	80077	80302	Peak_43315	5	.	80077	80302	0	3	1,150,1	0,4,224	2.15378	2.49792	0.51405

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1	14303	17326	Peak_96230	2	.	14303	17326	0	4	1,150,150,1	0,12,1591,3022	1.60466	1.71608	0.21683

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1	14303	17326	Peak_96230	2	.	14303	17326	0	4	1,150,150,1	0,12,1591,3022	1.60466	1.71608	0.21683

Num	21
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30
Name	naive_overlap_thresh
Thread	thread_Root
PID	35813

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

Start	2017-01-27 17:15:29
End	2017-01-27 17:16:54
Elapsed	00:01:25
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR2532030.nodup.pr1.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR2532030.nodup.pr2.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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--------------------
28283 (process ID) old priority 0, new priority 10
Waiting for 47 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270772.1	80077	80302	Peak_43315	5	.	2.15378	2.49792	0.51405

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270772.1	80077	80302	Peak_43315	5	.	2.15378	2.49792	0.51405

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1	14303	17326	Peak_96230	2	.	1.60466	1.71608	0.21683

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1	14303	17326	Peak_96230	2	.	1.60466	1.71608	0.21683

Num	22
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31
Name	blacklist_filter peak 1
Thread	thread_Root
PID	33850

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

Start	2017-01-27 17:16:56
End	2017-01-27 17:18:09
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.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--------------------
33854 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL383557.1	54713	54863	Peak_23839	40	.	4.14698	4.08901	1.34252	47

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/rep1/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL383557.1	54713	54863	Peak_23839	40	.	4.14698	4.08901	1.34252	47

Num	23
ID	task.report.peak2hammock.line_412.id_32
Name	peak2hammock
Thread	thread_Root
PID	39343

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

Start	2017-01-27 17:18:10
End	2017-01-27 17:18:26
Elapsed	00:00:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
39349 (process ID) old priority 0, new priority 10

Num	24
ID	task.report.peak2hammock.line_412.id_33
Name	peak2hammock
Thread	thread_Root
PID	40877

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

Start	2017-01-27 17:18:27
End	2017-01-27 17:18:47
Elapsed	00:00:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.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/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/peak/macs2/overlap/SRR2532030.nodup.tagAlign_x_SRR2532031.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
40881 (process ID) old priority 0, new priority 10

Num	25
ID	task.graphviz.report.line_97.id_34
Name	report
Thread	thread_Root
PID	42956

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

Start	2017-01-27 17:18:48
End	2017-01-27 17:19:05
Elapsed	00:00:17
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/Luo2015Data/H3K9ac/out/report/H3K9ac_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/report/H3K9ac_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/report/H3K9ac_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
42961 (process ID) old priority 0, new priority 10

Num	26
ID	task.report.pdf2png.line_379.id_39
Name	pdf2png
Thread	thread_Root
PID	42962

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

Start	2017-01-27 17:18:48
End	2017-01-27 17:19:04
Elapsed	00:00:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.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/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/H3K9ac/out/qc/rep1/SRR2532030.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
42970 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/ucsc_tools/3.0.9:/software/modulefiles/homer/default:/software/modulefiles/Matlab/R2014b
bool	allowEmpty	false
string[]	args	[-species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532030.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Luo2015Data/RawReadsFiles/SRR2532031.fastq.gz, -final_stage, idr, -histone, $]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
string	CPATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_cTVn8v
string	LANG	en_US.UTF-8
string	LIBRARY_PATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:ucsc_tools/3.0.9:homer/default:Matlab/R2014b
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
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/:/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/:/software/Matlab/R2014b/bin:/software/weblogo/2.8.2:/software/homer/default/bin:/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/:/software/samtools/samtools-1.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect:/software/ucsc_tools/3.0.9:/software/ucsc_tools/3.0.9/blat:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5:/users/imk1/perl5:/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/Luo2015Data/H3K9ac
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/Luo2015Data/H3K9ac
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	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SCREEN_Name	CTCF_2015
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 32898 22
string	SSH_CONNECTION	171.65.77.8 32898 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	39490.H3K9ac.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	9035
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope