BigDataScript report: atac.bds

Script file /srv/scratch/annashch/bds_atac/atac.bds
Program ID atac.bds.20160517_221535_875
Start time 2016-05-17 22:15:35
Run time 00:34:19.465
Tasks executed 2
Tasks failed 1
Tasks failed names 
macs2_atac rep1
Arguments* [-multimapping, 4, -out_dir, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq]
System* local
Cpus* 1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None
thread_21 thread_Root 
 atac.bds.20160517_221535_875_parallel_21/task.callpeak_macs2.macs2_atac_rep1.line_192.id_6
thread_22 thread_Root 
 atac.bds.20160517_221535_875_parallel_22/task.postalign_bed.xcor_rep2.line_165.id_7

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.callpeak_macs2.macs2_atac_rep1.line_192.id_6
Name macs2_atac rep1
Thread thread_21
PID 22905
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 2
Mem
Start 2016-05-17 22:15:37
End 2016-05-17 22:15:37
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig
Dependencies 
 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg
 
    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 22:15:42: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz']
# control file = None
# 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: 10000 bps
# Broad region calling is on
 
INFO  @ Tue, 17 May 2016 22:15:42: #1 read tag files... 
INFO  @ Tue, 17 May 2016 22:15:42: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 22:15:44:  1000000 
INFO  @ Tue, 17 May 2016 22:15:46:  2000000 
INFO  @ Tue, 17 May 2016 22:15:48:  3000000 
INFO  @ Tue, 17 May 2016 22:15:50:  4000000 
INFO  @ Tue, 17 May 2016 22:15:52:  5000000 
INFO  @ Tue, 17 May 2016 22:15:54:  6000000 
INFO  @ Tue, 17 May 2016 22:15:56:  7000000 
INFO  @ Tue, 17 May 2016 22:15:58:  8000000 
INFO  @ Tue, 17 May 2016 22:16:00:  9000000 
INFO  @ Tue, 17 May 2016 22:16:02:  10000000 
INFO  @ Tue, 17 May 2016 22:16:04:  11000000 
INFO  @ Tue, 17 May 2016 22:16:06:  12000000 
INFO  @ Tue, 17 May 2016 22:16:08:  13000000 
INFO  @ Tue, 17 May 2016 22:16:10:  14000000 
INFO  @ Tue, 17 May 2016 22:16:13:  15000000 
INFO  @ Tue, 17 May 2016 22:16:15:  16000000 
INFO  @ Tue, 17 May 2016 22:16:17:  17000000 
INFO  @ Tue, 17 May 2016 22:16:19:  18000000 
INFO  @ Tue, 17 May 2016 22:16:21:  19000000 
INFO  @ Tue, 17 May 2016 22:16:23:  20000000 
INFO  @ Tue, 17 May 2016 22:16:25:  21000000 
INFO  @ Tue, 17 May 2016 22:16:27:  22000000 
INFO  @ Tue, 17 May 2016 22:16:29:  23000000 
INFO  @ Tue, 17 May 2016 22:16:31:  24000000 
INFO  @ Tue, 17 May 2016 22:16:33:  25000000 
INFO  @ Tue, 17 May 2016 22:16:35:  26000000 
INFO  @ Tue, 17 May 2016 22:16:37:  27000000 
INFO  @ Tue, 17 May 2016 22:16:39:  28000000 
INFO  @ Tue, 17 May 2016 22:16:41:  29000000 
INFO  @ Tue, 17 May 2016 22:16:43:  30000000 
INFO  @ Tue, 17 May 2016 22:16:45:  31000000 
INFO  @ Tue, 17 May 2016 22:16:48:  32000000 
INFO  @ Tue, 17 May 2016 22:16:50:  33000000 
INFO  @ Tue, 17 May 2016 22:16:52:  34000000 
INFO  @ Tue, 17 May 2016 22:16:54:  35000000 
INFO  @ Tue, 17 May 2016 22:16:56:  36000000 
INFO  @ Tue, 17 May 2016 22:16:58:  37000000 
INFO  @ Tue, 17 May 2016 22:17:00:  38000000 
INFO  @ Tue, 17 May 2016 22:17:02:  39000000 
INFO  @ Tue, 17 May 2016 22:17:04:  40000000 
INFO  @ Tue, 17 May 2016 22:17:06:  41000000 
INFO  @ Tue, 17 May 2016 22:17:08:  42000000 
INFO  @ Tue, 17 May 2016 22:17:10:  43000000 
INFO  @ Tue, 17 May 2016 22:17:12:  44000000 
INFO  @ Tue, 17 May 2016 22:17:14:  45000000 
INFO  @ Tue, 17 May 2016 22:17:16:  46000000 
INFO  @ Tue, 17 May 2016 22:17:18:  47000000 
INFO  @ Tue, 17 May 2016 22:17:20:  48000000 
INFO  @ Tue, 17 May 2016 22:17:22:  49000000 
INFO  @ Tue, 17 May 2016 22:17:24:  50000000 
INFO  @ Tue, 17 May 2016 22:17:26:  51000000 
INFO  @ Tue, 17 May 2016 22:17:28:  52000000 
INFO  @ Tue, 17 May 2016 22:17:35: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 22:17:35: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 22:17:35: #1  total tags in treatment: 52989484 
INFO  @ Tue, 17 May 2016 22:17:35: #1 finished! 
INFO  @ Tue, 17 May 2016 22:17:35: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 22:17:35: #2 Skipped... 
INFO  @ Tue, 17 May 2016 22:17:35: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 22:17:35: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 22:17:35: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 22:17:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 22:17:35: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 22:20:04: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 22:23:58: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 22:24:01: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 22:24:04: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 22:24:07: Done! 
INFO  @ Tue, 17 May 2016 22:24:23: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz']
# control file = None
# 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: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 22:24:23: #1 read tag files... 
INFO  @ Tue, 17 May 2016 22:24:23: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 22:24:25:  1000000 
INFO  @ Tue, 17 May 2016 22:24:27:  2000000 
INFO  @ Tue, 17 May 2016 22:24:29:  3000000 
INFO  @ Tue, 17 May 2016 22:24:31:  4000000 
INFO  @ Tue, 17 May 2016 22:24:33:  5000000 
INFO  @ Tue, 17 May 2016 22:24:35:  6000000 
INFO  @ Tue, 17 May 2016 22:24:37:  7000000 
INFO  @ Tue, 17 May 2016 22:24:39:  8000000 
INFO  @ Tue, 17 May 2016 22:24:41:  9000000 
INFO  @ Tue, 17 May 2016 22:24:43:  10000000 
INFO  @ Tue, 17 May 2016 22:24:45:  11000000 
INFO  @ Tue, 17 May 2016 22:24:47:  12000000 
INFO  @ Tue, 17 May 2016 22:24:49:  13000000 
INFO  @ Tue, 17 May 2016 22:24:51:  14000000 
INFO  @ Tue, 17 May 2016 22:24:52:  15000000 
INFO  @ Tue, 17 May 2016 22:24:54:  16000000 
INFO  @ Tue, 17 May 2016 22:24:56:  17000000 
INFO  @ Tue, 17 May 2016 22:24:58:  18000000 
INFO  @ Tue, 17 May 2016 22:25:00:  19000000 
INFO  @ Tue, 17 May 2016 22:25:02:  20000000 
INFO  @ Tue, 17 May 2016 22:25:04:  21000000 
INFO  @ Tue, 17 May 2016 22:25:06:  22000000 
INFO  @ Tue, 17 May 2016 22:25:08:  23000000 
INFO  @ Tue, 17 May 2016 22:25:10:  24000000 
INFO  @ Tue, 17 May 2016 22:25:12:  25000000 
INFO  @ Tue, 17 May 2016 22:25:14:  26000000 
INFO  @ Tue, 17 May 2016 22:25:16:  27000000 
INFO  @ Tue, 17 May 2016 22:25:19:  28000000 
INFO  @ Tue, 17 May 2016 22:25:21:  29000000 
INFO  @ Tue, 17 May 2016 22:25:23:  30000000 
INFO  @ Tue, 17 May 2016 22:25:25:  31000000 
INFO  @ Tue, 17 May 2016 22:25:27:  32000000 
INFO  @ Tue, 17 May 2016 22:25:29:  33000000 
INFO  @ Tue, 17 May 2016 22:25:31:  34000000 
INFO  @ Tue, 17 May 2016 22:25:33:  35000000 
INFO  @ Tue, 17 May 2016 22:25:35:  36000000 
INFO  @ Tue, 17 May 2016 22:25:36:  37000000 
INFO  @ Tue, 17 May 2016 22:25:38:  38000000 
INFO  @ Tue, 17 May 2016 22:25:40:  39000000 
INFO  @ Tue, 17 May 2016 22:25:42:  40000000 
INFO  @ Tue, 17 May 2016 22:25:44:  41000000 
INFO  @ Tue, 17 May 2016 22:25:46:  42000000 
INFO  @ Tue, 17 May 2016 22:25:48:  43000000 
INFO  @ Tue, 17 May 2016 22:25:50:  44000000 
INFO  @ Tue, 17 May 2016 22:25:52:  45000000 
INFO  @ Tue, 17 May 2016 22:25:54:  46000000 
INFO  @ Tue, 17 May 2016 22:25:56:  47000000 
INFO  @ Tue, 17 May 2016 22:25:58:  48000000 
INFO  @ Tue, 17 May 2016 22:26:00:  49000000 
INFO  @ Tue, 17 May 2016 22:26:02:  50000000 
INFO  @ Tue, 17 May 2016 22:26:04:  51000000 
INFO  @ Tue, 17 May 2016 22:26:06:  52000000 
INFO  @ Tue, 17 May 2016 22:26:12: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 22:26:12: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 22:26:12: #1  total tags in treatment: 52989484 
INFO  @ Tue, 17 May 2016 22:26:12: #1 finished! 
INFO  @ Tue, 17 May 2016 22:26:12: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 22:26:12: #2 Skipped... 
INFO  @ Tue, 17 May 2016 22:26:12: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 22:26:12: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 22:26:12: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 22:26:12: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 22:26:12: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 22:26:12: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 22:28:46: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 22:28:46: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 22:28:46: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 22:28:46: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 22:28:46: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 22:36:16: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 22:36:18: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 22:36:21: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 22:36:22: Done! 
INFO  @ Tue, 17 May 2016 22:36:26: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 22:38:15: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 22:38:54: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 22:39:34: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 22:45:40: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 22:49:54: Finished 'FE'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
invalid unsigned integer: "58682461chr1"
Num 2
ID task.postalign_bed.xcor_rep2.line_165.id_7
Name xcor rep2
Thread thread_22
PID 22907
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 1
Mem
Start 2016-05-17 22:15:37
End 2016-05-17 22:49:13
Elapsed 00:33:36
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
Output files /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies 
 
# SYS command. line 167

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc
 
   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpWhsSbi/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign59ea3b1f3da
done. read 22207786 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1296254 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.24174066170555 
Top 3 estimates for fragment length 0 
Window half size 500 
Phantom peak location 80 
Phantom peak Correlation 0.2620464 
Normalized Strand cross-correlation coefficient (NSC) 1.864918 
Relative Strand Cross correlation Coefficient (RSC) 0.846658 
Phantom Peak Quality Tag 0 
null device 
          1 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
Loading required package: caTools

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /bin/sh
string _JAVA_OPTIONS -Xms256M -Xmx512M -XX:ParallelGCThreads=1
bool allowEmpty false
string[] args [-multimapping, 4, -out_dir, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq]
string BASSETDIR /srv/scratch/annashch/Basset
bool canFail false
int cpus 1
int cpusLocal 48
string CRC /srv/scratch/annashch/crc
int day 86400
string DEEPLEARN_SCRIPTS_DIR /srv/scratch/annashch/deeplearning_avanti
string DEEPLIFT_DIR /srv/scratch/annashch/deeplift/deeplift
real E 2.718281828459045
string EIGEN /mnt/lab_data/montgomery/shared/Eigen
string ENHANCER_SCRIPTS_DIR /srv/scratch/annashch/enhancer_prediction_code
int G 1073741824
string HOME /users/annashch/
int hour 3600
int K 1024
string KERAS_DIR /users/annashch/keras
string LANG en_US.UTF-8
string LD_LIBRARY_PATH /lib/x86_64-linux-gnu:/usr/local/cudnn/lib64:
string LOADEDMODULES
string LOGNAME annashch
string LUACPATH /srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:
string LUAPATH /srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:
int M 1048576
string MAIL /var/mail/annashch
string MALLOC_ARENA_MAX 4
string MAX_JAVA_MEM 20G
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string MODULESHOME /software/env_module/3.2.10
string node
string OLDPWD /srv/scratch/annashch
int P 1125899906842624
string PATH /srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin
real PI 3.141592653589793
string ppwd /srv/scratch/annashch/output
string programName atac.bds
string programPath /srv/scratch/annashch/bds_atac/atac.bds
string PWD /srv/scratch/annashch/output
string PYTHONPATH /users/annashch/keras:/srv/scratch/annashch/Basset/src:/users/annashch/keras:/srv/scratch/annashch/Basset/src:
string QT_QPA_PLATFORMTHEME appmenu-qt5
string queue
int retry 0
string SHELL /bin/bash
string SHLVL 2
string SSH_CLIENT 10.0.2.3 44081 22
string SSH_CONNECTION 10.0.2.3 44081 10.0.2.8 22
string SSH_TTY /dev/pts/131
string STY 7366.pts-131.kali
string system local
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#57:co#205: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:us=\\E[4m:ue=\\E[24m:so=\\E[3m:\\\n\t:se=\\E[23m:mb=\\E[5m:md=\\E[1m:mr=\\E[7m:me=\\E[m:ms:\\\n\t:Co#8:pa#64:AF=\\E[3%dm:AB=\\E[4%dm:op=\\E[39;49m:AX:\\\n\t:vb=\\Eg:G0:as=\\E(0:ae=\\E(B:\\\n\t:ac=\\140\\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{||}}~~..--++,,hhII00:\\\n\t:po=\\E[5i:pf=\\E[4i:Km=\\E[M:k0=\\E[10~:k1=\\EOP:k2=\\EOQ:\\\n\t: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:F3=\\E[1;2P:F4=\\E[1;2Q:F5=\\E[1;2R:F6=\\E[1;2S:\\\n\t:F7=\\E[15;2~:F8=\\E[17;2~:F9=\\E[18;2~:FA=\\E[19;2~:kb=:\\\n\t:K2=\\EOE:kB=\\E[Z:kF=\\E[1;2B:kR=\\E[1;2A:*4=\\E[3;2~:\\\n\t:*7=\\E[1;2F:#2=\\E[1;2H:#3=\\E[2;2~:#4=\\E[1;2D:%c=\\E[6;2~:\\\n\t:%e=\\E[5;2~:%i=\\E[1;2C:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:\\\n\t:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:\\\n\t:kd=\\EOB:kr=\\EOC:kl=\\EOD:km:
int timeout -1
string USER annashch
string UTIL_SCRIPTS_DIR /srv/scratch/annashch/av_scripts
int walltimeout 8640000
int week 604800
string WINDOW 0
string XDG_RUNTIME_DIR /run/user/1091
string XDG_SESSION_ID 897