Script file	/srv/scratch/annashch/bds_atac/atac.bds
Program ID	atac.bds.20160516_202756_386
Start time	2016-05-16 20:27:56
Run time	1 day 04:14:19.372
Tasks executed	61
Tasks failed	0
Tasks failed names
Arguments*	[-multimapping, 4, -out_dir, 4x_experiments/baseChroms_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, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, /srv/scratch/annashch/refs/wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq]
System*	local
Cpus*	1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160516_202756_386/task.postalign_bed.pool_tag_reps.line_405.id_36 atac.bds.20160516_202756_386/task.postalign_bed.pool_tag_reps_pr1.line_405.id_37 atac.bds.20160516_202756_386/task.postalign_bed.pool_tag_reps_pr2.line_405.id_38 atac.bds.20160516_202756_386/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_39 atac.bds.20160516_202756_386/task.callpeak_macs2.macs2_atac_pooled.line_192.id_40 atac.bds.20160516_202756_386/task.callpeak_macs2.macs2_atac_ppr1.pval0.1.line_192.id_41 atac.bds.20160516_202756_386/task.callpeak_macs2.macs2_atac_ppr2.pval0.1.line_192.id_42 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_43 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_44 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_45 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_46 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_47 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_48 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_49 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_50 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_51 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_52 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_53 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_54 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_55 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_56 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_57 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_58 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_59 atac.bds.20160516_202756_386/task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_60 atac.bds.20160516_202756_386/task.callpeak_etc.naive_overlap_thresh_peak.line_125.id_61 atac.bds.20160516_202756_386/task.callpeak_etc.naive_overlap_thresh_gpeak.line_125.id_62 atac.bds.20160516_202756_386/task.idr.idr2_rep1_rep2.line_72.id_63 atac.bds.20160516_202756_386/task.idr.idr2_rep1_pr.line_72.id_64 atac.bds.20160516_202756_386/task.idr.idr2_rep2_pr.line_72.id_65 atac.bds.20160516_202756_386/task.idr.idr2_ppr.line_72.id_66
thread_21	thread_Root	atac.bds.20160516_202756_386_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_131.id_7 atac.bds.20160516_202756_386_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9 atac.bds.20160516_202756_386_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_23 atac.bds.20160516_202756_386_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_24 atac.bds.20160516_202756_386_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_25 atac.bds.20160516_202756_386_parallel_21/task.postalign_bed.spr_PE_rep2.line_248.id_26 atac.bds.20160516_202756_386_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_27 atac.bds.20160516_202756_386_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_28 atac.bds.20160516_202756_386_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_29 atac.bds.20160516_202756_386_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_30 atac.bds.20160516_202756_386_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_31 atac.bds.20160516_202756_386_parallel_21/task.callpeak_macs2.macs2_atac_rep2_pr1.pval0.1.line_192.id_32 atac.bds.20160516_202756_386_parallel_21/task.callpeak_macs2.macs2_atac_rep2_pr2.pval0.1.line_192.id_33 atac.bds.20160516_202756_386_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_34 atac.bds.20160516_202756_386_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_35
thread_20	thread_Root	atac.bds.20160516_202756_386_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_131.id_6 atac.bds.20160516_202756_386_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160516_202756_386_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_10 atac.bds.20160516_202756_386_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_11 atac.bds.20160516_202756_386_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12 atac.bds.20160516_202756_386_parallel_20/task.postalign_bed.spr_PE_rep1.line_248.id_13 atac.bds.20160516_202756_386_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_14 atac.bds.20160516_202756_386_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_15 atac.bds.20160516_202756_386_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_16 atac.bds.20160516_202756_386_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_17 atac.bds.20160516_202756_386_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_18 atac.bds.20160516_202756_386_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr1.pval0.1.line_192.id_19 atac.bds.20160516_202756_386_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr2.pval0.1.line_192.id_20 atac.bds.20160516_202756_386_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_21 atac.bds.20160516_202756_386_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_22

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep1.line_131.id_6
Name	bowtie2_PE rep1
Thread	thread_20
PID	1492

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

Start	2016-05-16 20:27:57
End	2016-05-17 06:28:41
Elapsed	10:00:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 133

 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 135

 bowtie2 -k 4 -X2000 --mm --threads 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix \
			-1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz -2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz 2>/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep2.line_131.id_7
Name	bowtie2_PE rep2
Thread	thread_21
PID	1497

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

Start	2016-05-16 20:27:57
End	2016-05-17 11:40:13
Elapsed	15:12:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 133

 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 135

 bowtie2 -k 4 -X2000 --mm --threads 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix \
			-1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz -2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz 2>/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8
Name	dedup_bam_PE rep1
Thread	thread_20
PID	6479

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

Start	2016-05-17 06:28:42
End	2016-05-17 11:44:44
Elapsed	05:16:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

 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 228

 samtools view -F 524 -f 2 -u /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.multi

# SYS command. line 229

 samtools view -h /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.multi.bam | $(which assign_multimappers.py) -k 4 --paired-end | samtools view -bS - > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam

# SYS command. line 230

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.multi.bam

# SYS command. line 237

 samtools fixmate -r /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 243

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

 mv /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			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{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/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 77 files...
[bam_sort_core] merging from 42 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 09:51:52 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.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
[Tue May 17 09:51:52 PDT 2016] Executing as annashch@kali on Linux 3.19.0-25-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-17 09:51:52	MarkDuplicates	Start of doWork freeMemory: 254891072; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 09:51:52	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 09:51:52	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 09:51:58	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:124,037,702
INFO	2016-05-17 09:51:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:52:03	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr11:115,637,405
INFO	2016-05-17 09:52:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:52:08	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    5s.  Last read position: chr12:94,683,918
INFO	2016-05-17 09:52:08	MarkDuplicates	Tracking 22 as yet unmatched pairs. 22 records in RAM.
INFO	2016-05-17 09:52:14	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    5s.  Last read position: chr14:24,379,420
INFO	2016-05-17 09:52:14	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:52:22	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    8s.  Last read position: chr15:66,080,113
INFO	2016-05-17 09:52:22	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-17 09:52:30	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    7s.  Last read position: chr17:7,978,687
INFO	2016-05-17 09:52:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:52:37	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    7s.  Last read position: chr18:46,454,458
INFO	2016-05-17 09:52:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:52:42	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    4s.  Last read position: chr1:566,091
INFO	2016-05-17 09:52:42	MarkDuplicates	Tracking 4620 as yet unmatched pairs. 4620 records in RAM.
INFO	2016-05-17 09:52:47	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    4s.  Last read position: chr1:48,193,021
INFO	2016-05-17 09:52:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:52:51	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    4s.  Last read position: chr1:181,189,461
INFO	2016-05-17 09:52:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:52:56	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    4s.  Last read position: chr20:47,565,245
INFO	2016-05-17 09:52:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:53:02	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    5s.  Last read position: chr2:42,569,635
INFO	2016-05-17 09:53:02	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 09:53:16	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:   14s.  Last read position: chr2:180,123,941
INFO	2016-05-17 09:53:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:53:21	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    5s.  Last read position: chr3:48,651,661
INFO	2016-05-17 09:53:21	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-17 09:53:41	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:   19s.  Last read position: chr3:179,372,260
INFO	2016-05-17 09:53:41	MarkDuplicates	Tracking 18 as yet unmatched pairs. 18 records in RAM.
INFO	2016-05-17 09:53:46	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    4s.  Last read position: chr4:134,904,122
INFO	2016-05-17 09:53:46	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:53:51	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    5s.  Last read position: chr5:92,915,018
INFO	2016-05-17 09:53:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:53:55	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    4s.  Last read position: chr6:15,326,693
INFO	2016-05-17 09:53:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:54:02	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    6s.  Last read position: chr6:146,734,937
INFO	2016-05-17 09:54:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:54:10	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    8s.  Last read position: chr7:112,634,846
INFO	2016-05-17 09:54:10	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:54:15	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    4s.  Last read position: chr8:98,739,802
INFO	2016-05-17 09:54:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:54:20	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    4s.  Last read position: chr9:110,495,149
INFO	2016-05-17 09:54:20	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 09:54:25	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,099
INFO	2016-05-17 09:54:25	MarkDuplicates	Tracking 11674 as yet unmatched pairs. 11674 records in RAM.
INFO	2016-05-17 09:54:29	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,084
INFO	2016-05-17 09:54:29	MarkDuplicates	Tracking 45020 as yet unmatched pairs. 45020 records in RAM.
INFO	2016-05-17 09:54:37	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,914
INFO	2016-05-17 09:54:37	MarkDuplicates	Tracking 32368 as yet unmatched pairs. 32368 records in RAM.
INFO	2016-05-17 09:54:41	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    4s.  Last read position: chrM:4,986
INFO	2016-05-17 09:54:41	MarkDuplicates	Tracking 38892 as yet unmatched pairs. 38892 records in RAM.
INFO	2016-05-17 09:54:46	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,229
INFO	2016-05-17 09:54:46	MarkDuplicates	Tracking 26570 as yet unmatched pairs. 26570 records in RAM.
INFO	2016-05-17 09:54:54	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    8s.  Last read position: chrM:7,475
INFO	2016-05-17 09:54:54	MarkDuplicates	Tracking 32192 as yet unmatched pairs. 32192 records in RAM.
INFO	2016-05-17 09:54:58	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    4s.  Last read position: chrM:8,408
INFO	2016-05-17 09:54:58	MarkDuplicates	Tracking 20202 as yet unmatched pairs. 20202 records in RAM.
INFO	2016-05-17 09:55:19	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:   20s.  Last read position: chrM:9,300
INFO	2016-05-17 09:55:19	MarkDuplicates	Tracking 25304 as yet unmatched pairs. 25304 records in RAM.
INFO	2016-05-17 09:55:24	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,289
INFO	2016-05-17 09:55:24	MarkDuplicates	Tracking 38820 as yet unmatched pairs. 38820 records in RAM.
INFO	2016-05-17 09:55:30	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,227
INFO	2016-05-17 09:55:30	MarkDuplicates	Tracking 32356 as yet unmatched pairs. 32356 records in RAM.
INFO	2016-05-17 09:55:39	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    9s.  Last read position: chrM:11,970
INFO	2016-05-17 09:55:39	MarkDuplicates	Tracking 30662 as yet unmatched pairs. 30662 records in RAM.
INFO	2016-05-17 09:55:44	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,870
INFO	2016-05-17 09:55:44	MarkDuplicates	Tracking 33320 as yet unmatched pairs. 33320 records in RAM.
INFO	2016-05-17 09:55:48	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,910
INFO	2016-05-17 09:55:48	MarkDuplicates	Tracking 23550 as yet unmatched pairs. 23550 records in RAM.
INFO	2016-05-17 09:55:52	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,997
INFO	2016-05-17 09:55:52	MarkDuplicates	Tracking 32188 as yet unmatched pairs. 32188 records in RAM.
INFO	2016-05-17 09:55:56	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,726
INFO	2016-05-17 09:55:56	MarkDuplicates	Tracking 34172 as yet unmatched pairs. 34172 records in RAM.
INFO	2016-05-17 09:56:00	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    4s.  Last read position: chrX:42,605,892
INFO	2016-05-17 09:56:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:56:07	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr10:52,502,019
INFO	2016-05-17 09:56:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:56:11	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr10:119,866,793
INFO	2016-05-17 09:56:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 09:56:16	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr11:52,885,946
INFO	2016-05-17 09:56:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:56:21	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr11:100,143,462
INFO	2016-05-17 09:56:21	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-17 09:56:26	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr12:53,707,268
INFO	2016-05-17 09:56:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:56:30	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:4,770,699
INFO	2016-05-17 09:56:30	MarkDuplicates	Tracking 58 as yet unmatched pairs. 58 records in RAM.
INFO	2016-05-17 09:56:41	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:   10s.  Last read position: mm9_chr13:70,776,891
INFO	2016-05-17 09:56:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:56:45	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:26,689,117
INFO	2016-05-17 09:56:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 09:56:50	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:92,516,097
INFO	2016-05-17 09:56:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:56:55	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr15:38,426,619
INFO	2016-05-17 09:56:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:56:59	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr15:100,779,700
INFO	2016-05-17 09:56:59	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:57:04	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr16:61,355,509
INFO	2016-05-17 09:57:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:57:11	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr17:33,896,668
INFO	2016-05-17 09:57:11	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:57:15	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr18:4,826,779
INFO	2016-05-17 09:57:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:57:20	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr18:68,913,216
INFO	2016-05-17 09:57:20	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:57:24	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr19:34,344,969
INFO	2016-05-17 09:57:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:57:29	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:24,618,772
INFO	2016-05-17 09:57:29	MarkDuplicates	Tracking 21696 as yet unmatched pairs. 21696 records in RAM.
INFO	2016-05-17 09:57:33	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:40s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,619,874
INFO	2016-05-17 09:57:33	MarkDuplicates	Tracking 45562 as yet unmatched pairs. 45562 records in RAM.
INFO	2016-05-17 09:57:38	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr1:24,620,908
INFO	2016-05-17 09:57:38	MarkDuplicates	Tracking 29752 as yet unmatched pairs. 29752 records in RAM.
INFO	2016-05-17 09:57:48	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    9s.  Last read position: mm9_chr1:24,622,145
INFO	2016-05-17 09:57:48	MarkDuplicates	Tracking 21304 as yet unmatched pairs. 21304 records in RAM.
INFO	2016-05-17 09:58:06	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:   18s.  Last read position: mm9_chr1:63,153,101
INFO	2016-05-17 09:58:06	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 09:58:14	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr1:137,364,792
INFO	2016-05-17 09:58:14	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 09:58:21	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr1:196,564,823
INFO	2016-05-17 09:58:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:58:27	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr2:44,145,660
INFO	2016-05-17 09:58:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:58:34	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr2:113,651,408
INFO	2016-05-17 09:58:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:58:41	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr2:167,299,420
INFO	2016-05-17 09:58:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:58:48	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:06:56s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr3:69,531,239
INFO	2016-05-17 09:58:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:58:56	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr3:132,169,185
INFO	2016-05-17 09:58:56	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:59:01	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr4:53,607,215
INFO	2016-05-17 09:59:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 09:59:05	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr4:125,669,750
INFO	2016-05-17 09:59:05	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-17 09:59:10	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:07:17s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr5:31,754,152
INFO	2016-05-17 09:59:10	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:59:14	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr5:104,453,956
INFO	2016-05-17 09:59:14	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:59:19	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:4,120,368
INFO	2016-05-17 09:59:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:59:23	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:83,724,260
INFO	2016-05-17 09:59:23	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-17 09:59:31	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr6:142,863,132
INFO	2016-05-17 09:59:31	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-17 09:59:40	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:    9s.  Last read position: mm9_chr7:75,502,584
INFO	2016-05-17 09:59:40	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 09:59:47	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr7:135,567,887
INFO	2016-05-17 09:59:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:59:56	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    8s.  Last read position: mm9_chr8:59,599,710
INFO	2016-05-17 09:59:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 10:00:02	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:08:09s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr8:121,430,671
INFO	2016-05-17 10:00:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 10:00:06	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr9:56,923,732
INFO	2016-05-17 10:00:06	MarkDuplicates	Tracking 28 as yet unmatched pairs. 28 records in RAM.
INFO	2016-05-17 10:00:13	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr9:110,975,584
INFO	2016-05-17 10:00:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 10:00:18	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:515
INFO	2016-05-17 10:00:18	MarkDuplicates	Tracking 62280 as yet unmatched pairs. 62280 records in RAM.
INFO	2016-05-17 10:00:23	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:08:30s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:1,199
INFO	2016-05-17 10:00:23	MarkDuplicates	Tracking 49120 as yet unmatched pairs. 49120 records in RAM.
INFO	2016-05-17 10:00:31	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:1,942
INFO	2016-05-17 10:00:31	MarkDuplicates	Tracking 35716 as yet unmatched pairs. 35716 records in RAM.
INFO	2016-05-17 10:00:34	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,726
INFO	2016-05-17 10:00:34	MarkDuplicates	Tracking 38700 as yet unmatched pairs. 38700 records in RAM.
INFO	2016-05-17 10:00:38	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:08:46s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:3,321
INFO	2016-05-17 10:00:38	MarkDuplicates	Tracking 52696 as yet unmatched pairs. 52696 records in RAM.
INFO	2016-05-17 10:00:42	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:3,919
INFO	2016-05-17 10:00:42	MarkDuplicates	Tracking 43340 as yet unmatched pairs. 43340 records in RAM.
INFO	2016-05-17 10:00:46	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,550
INFO	2016-05-17 10:00:46	MarkDuplicates	Tracking 39120 as yet unmatched pairs. 39120 records in RAM.
INFO	2016-05-17 10:00:50	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:08:57s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,372
INFO	2016-05-17 10:00:50	MarkDuplicates	Tracking 35288 as yet unmatched pairs. 35288 records in RAM.
INFO	2016-05-17 10:00:53	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:09:01s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,944
INFO	2016-05-17 10:00:53	MarkDuplicates	Tracking 58104 as yet unmatched pairs. 58104 records in RAM.
INFO	2016-05-17 10:01:09	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:09:16s.  Time for last 1,000,000:   15s.  Last read position: mm9_chrM:6,691
INFO	2016-05-17 10:01:09	MarkDuplicates	Tracking 37794 as yet unmatched pairs. 37794 records in RAM.
INFO	2016-05-17 10:01:12	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:7,992
INFO	2016-05-17 10:01:12	MarkDuplicates	Tracking 23856 as yet unmatched pairs. 23856 records in RAM.
INFO	2016-05-17 10:01:17	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:9,108
INFO	2016-05-17 10:01:17	MarkDuplicates	Tracking 31516 as yet unmatched pairs. 31516 records in RAM.
INFO	2016-05-17 10:01:21	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:10,526
INFO	2016-05-17 10:01:21	MarkDuplicates	Tracking 18530 as yet unmatched pairs. 18530 records in RAM.
INFO	2016-05-17 10:01:25	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:09:32s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,312
INFO	2016-05-17 10:01:25	MarkDuplicates	Tracking 62074 as yet unmatched pairs. 62074 records in RAM.
INFO	2016-05-17 10:01:29	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,058
INFO	2016-05-17 10:01:29	MarkDuplicates	Tracking 39790 as yet unmatched pairs. 39790 records in RAM.
INFO	2016-05-17 10:01:32	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,642
INFO	2016-05-17 10:01:32	MarkDuplicates	Tracking 46132 as yet unmatched pairs. 46132 records in RAM.
INFO	2016-05-17 10:01:36	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,232
INFO	2016-05-17 10:01:36	MarkDuplicates	Tracking 46396 as yet unmatched pairs. 46396 records in RAM.
INFO	2016-05-17 10:01:40	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:09:47s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,915
INFO	2016-05-17 10:01:40	MarkDuplicates	Tracking 48910 as yet unmatched pairs. 48910 records in RAM.
INFO	2016-05-17 10:01:44	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,511
INFO	2016-05-17 10:01:44	MarkDuplicates	Tracking 42890 as yet unmatched pairs. 42890 records in RAM.
INFO	2016-05-17 10:01:47	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,078
INFO	2016-05-17 10:01:47	MarkDuplicates	Tracking 53644 as yet unmatched pairs. 53644 records in RAM.
INFO	2016-05-17 10:01:54	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:10:01s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:16,110
INFO	2016-05-17 10:01:54	MarkDuplicates	Tracking 10702 as yet unmatched pairs. 10702 records in RAM.
INFO	2016-05-17 10:01:58	MarkDuplicates	Read 100969484 records. 0 pairs never matched.
INFO	2016-05-17 10:02:07	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3445665016; totalMemory: 3472359424; maxMemory: 3817865216
INFO	2016-05-17 10:02:07	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 10:02:07	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 10:02:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 10:02:56	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 10:02:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2499379072; totalMemory: 3480748032; maxMemory: 3817865216
INFO	2016-05-17 10:02:59	MarkDuplicates	Marking 42881172 records as duplicates.
INFO	2016-05-17 10:02:59	MarkDuplicates	Found 7658694 optical duplicate clusters.
INFO	2016-05-17 10:05:01	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:00s.  Time for last 10,000,000:  120s.  Last read position: chr1:181,189,461
INFO	2016-05-17 10:07:06	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:05s.  Time for last 10,000,000:  125s.  Last read position: chr7:112,634,846
INFO	2016-05-17 10:08:59	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:58s.  Time for last 10,000,000:  112s.  Last read position: chrM:9,300
INFO	2016-05-17 10:10:53	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:52s.  Time for last 10,000,000:  113s.  Last read position: mm9_chr10:119,866,793
INFO	2016-05-17 10:12:59	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:09:59s.  Time for last 10,000,000:  126s.  Last read position: mm9_chr16:61,355,509
INFO	2016-05-17 10:14:58	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:11:58s.  Time for last 10,000,000:  119s.  Last read position: mm9_chr1:137,364,792
INFO	2016-05-17 10:17:04	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:14:04s.  Time for last 10,000,000:  125s.  Last read position: mm9_chr5:104,453,956
INFO	2016-05-17 10:19:11	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:16:11s.  Time for last 10,000,000:  127s.  Last read position: mm9_chrM:515
INFO	2016-05-17 10:20:58	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:17:57s.  Time for last 10,000,000:  106s.  Last read position: mm9_chrM:7,992
INFO	2016-05-17 10:22:44	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:19:43s.  Time for last 10,000,000:  105s.  Last read position: mm9_chrM:16,110
INFO	2016-05-17 10:22:56	MarkDuplicates	Before output close freeMemory: 3536572600; totalMemory: 3566731264; maxMemory: 3817865216
INFO	2016-05-17 10:22:56	MarkDuplicates	After output close freeMemory: 3536571544; totalMemory: 3566731264; maxMemory: 3817865216
[Tue May 17 10:22:56 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 31.07 minutes.
Runtime.totalMemory()=3566731264
[bam_sort_core] merging from 42 files...

Num	4
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9
Name	dedup_bam_PE rep2
Thread	thread_21
PID	13328

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

Start	2016-05-17 11:40:14
End	2016-05-17 20:42:46
Elapsed	09:02:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

 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 228

 samtools view -F 524 -f 2 -u /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.multi

# SYS command. line 229

 samtools view -h /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.multi.bam | $(which assign_multimappers.py) -k 4 --paired-end | samtools view -bS - > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam

# SYS command. line 230

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.multi.bam

# SYS command. line 237

 samtools fixmate -r /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 243

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

 mv /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			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{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/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 153 files...
[bam_sort_core] merging from 72 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 17:48:32 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.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
[Tue May 17 17:48:32 PDT 2016] Executing as annashch@kali on Linux 3.19.0-25-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-17 17:48:32	MarkDuplicates	Start of doWork freeMemory: 254891216; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 17:48:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 17:48:32	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 17:48:40	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    8s.  Last read position: chr11:60,150,857
INFO	2016-05-17 17:48:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:48:46	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    5s.  Last read position: chr12:101,691,695
INFO	2016-05-17 17:48:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:48:53	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    6s.  Last read position: chr14:91,527,069
INFO	2016-05-17 17:48:53	MarkDuplicates	Tracking 20 as yet unmatched pairs. 20 records in RAM.
INFO	2016-05-17 17:48:59	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    5s.  Last read position: chr17:5,389,860
INFO	2016-05-17 17:48:59	MarkDuplicates	Tracking 20 as yet unmatched pairs. 20 records in RAM.
INFO	2016-05-17 17:49:03	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    4s.  Last read position: chr19:18,392,482
INFO	2016-05-17 17:49:03	MarkDuplicates	Tracking 38 as yet unmatched pairs. 38 records in RAM.
INFO	2016-05-17 17:49:09	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    5s.  Last read position: chr1:565,632
INFO	2016-05-17 17:49:09	MarkDuplicates	Tracking 50618 as yet unmatched pairs. 50618 records in RAM.
INFO	2016-05-17 17:49:13	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    3s.  Last read position: chr1:567,590
INFO	2016-05-17 17:49:13	MarkDuplicates	Tracking 6632 as yet unmatched pairs. 6632 records in RAM.
INFO	2016-05-17 17:49:17	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    4s.  Last read position: chr1:569,886
INFO	2016-05-17 17:49:17	MarkDuplicates	Tracking 16004 as yet unmatched pairs. 16004 records in RAM.
INFO	2016-05-17 17:49:23	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    6s.  Last read position: chr1:112,798,446
INFO	2016-05-17 17:49:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:49:27	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    4s.  Last read position: chr20:50,673,228
INFO	2016-05-17 17:49:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:49:33	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    6s.  Last read position: chr2:120,968,310
INFO	2016-05-17 17:49:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:49:37	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    4s.  Last read position: chr3:46,734,460
INFO	2016-05-17 17:49:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:49:42	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    4s.  Last read position: chr4:41,452,484
INFO	2016-05-17 17:49:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:49:49	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    7s.  Last read position: chr5:84,357,600
INFO	2016-05-17 17:49:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:50:06	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:   17s.  Last read position: chr6:8,972,418
INFO	2016-05-17 17:50:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:50:11	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    4s.  Last read position: chr7:38,670,883
INFO	2016-05-17 17:50:11	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 17:50:15	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    4s.  Last read position: chr8:96,376,805
INFO	2016-05-17 17:50:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:50:19	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    4s.  Last read position: chrM:29
INFO	2016-05-17 17:50:19	MarkDuplicates	Tracking 30028 as yet unmatched pairs. 30028 records in RAM.
INFO	2016-05-17 17:50:25	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    5s.  Last read position: chrM:572
INFO	2016-05-17 17:50:25	MarkDuplicates	Tracking 21424 as yet unmatched pairs. 21424 records in RAM.
INFO	2016-05-17 17:50:29	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,336
INFO	2016-05-17 17:50:29	MarkDuplicates	Tracking 66076 as yet unmatched pairs. 66076 records in RAM.
INFO	2016-05-17 17:50:33	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,335
INFO	2016-05-17 17:50:33	MarkDuplicates	Tracking 66536 as yet unmatched pairs. 66536 records in RAM.
INFO	2016-05-17 17:50:37	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,851
INFO	2016-05-17 17:50:37	MarkDuplicates	Tracking 68770 as yet unmatched pairs. 68770 records in RAM.
INFO	2016-05-17 17:50:44	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,241
INFO	2016-05-17 17:50:44	MarkDuplicates	Tracking 100870 as yet unmatched pairs. 100870 records in RAM.
INFO	2016-05-17 17:50:47	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,487
INFO	2016-05-17 17:50:47	MarkDuplicates	Tracking 27870 as yet unmatched pairs. 27870 records in RAM.
INFO	2016-05-17 17:50:52	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,784
INFO	2016-05-17 17:50:52	MarkDuplicates	Tracking 54398 as yet unmatched pairs. 54398 records in RAM.
INFO	2016-05-17 17:50:55	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,067
INFO	2016-05-17 17:50:55	MarkDuplicates	Tracking 68038 as yet unmatched pairs. 68038 records in RAM.
INFO	2016-05-17 17:51:02	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    6s.  Last read position: chrM:4,526
INFO	2016-05-17 17:51:02	MarkDuplicates	Tracking 48084 as yet unmatched pairs. 48084 records in RAM.
INFO	2016-05-17 17:51:06	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,913
INFO	2016-05-17 17:51:06	MarkDuplicates	Tracking 54040 as yet unmatched pairs. 54040 records in RAM.
INFO	2016-05-17 17:51:11	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,309
INFO	2016-05-17 17:51:11	MarkDuplicates	Tracking 37570 as yet unmatched pairs. 37570 records in RAM.
INFO	2016-05-17 17:51:27	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:   15s.  Last read position: chrM:5,786
INFO	2016-05-17 17:51:27	MarkDuplicates	Tracking 32448 as yet unmatched pairs. 32448 records in RAM.
INFO	2016-05-17 17:51:31	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,201
INFO	2016-05-17 17:51:31	MarkDuplicates	Tracking 38274 as yet unmatched pairs. 38274 records in RAM.
INFO	2016-05-17 17:51:35	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,482
INFO	2016-05-17 17:51:35	MarkDuplicates	Tracking 36498 as yet unmatched pairs. 36498 records in RAM.
INFO	2016-05-17 17:51:39	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,009
INFO	2016-05-17 17:51:39	MarkDuplicates	Tracking 38364 as yet unmatched pairs. 38364 records in RAM.
INFO	2016-05-17 17:51:43	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,503
INFO	2016-05-17 17:51:43	MarkDuplicates	Tracking 100062 as yet unmatched pairs. 100062 records in RAM.
INFO	2016-05-17 17:51:46	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,822
INFO	2016-05-17 17:51:46	MarkDuplicates	Tracking 44048 as yet unmatched pairs. 44048 records in RAM.
INFO	2016-05-17 17:51:50	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,156
INFO	2016-05-17 17:51:50	MarkDuplicates	Tracking 62916 as yet unmatched pairs. 62916 records in RAM.
INFO	2016-05-17 17:51:56	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    5s.  Last read position: chrM:8,583
INFO	2016-05-17 17:51:56	MarkDuplicates	Tracking 31898 as yet unmatched pairs. 31898 records in RAM.
INFO	2016-05-17 17:52:00	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,940
INFO	2016-05-17 17:52:00	MarkDuplicates	Tracking 55758 as yet unmatched pairs. 55758 records in RAM.
INFO	2016-05-17 17:52:03	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,219
INFO	2016-05-17 17:52:03	MarkDuplicates	Tracking 38572 as yet unmatched pairs. 38572 records in RAM.
INFO	2016-05-17 17:52:07	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,587
INFO	2016-05-17 17:52:07	MarkDuplicates	Tracking 30062 as yet unmatched pairs. 30062 records in RAM.
INFO	2016-05-17 17:52:11	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,867
INFO	2016-05-17 17:52:11	MarkDuplicates	Tracking 88596 as yet unmatched pairs. 88596 records in RAM.
INFO	2016-05-17 17:52:14	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,194
INFO	2016-05-17 17:52:14	MarkDuplicates	Tracking 56698 as yet unmatched pairs. 56698 records in RAM.
INFO	2016-05-17 17:52:20	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    6s.  Last read position: chrM:10,462
INFO	2016-05-17 17:52:20	MarkDuplicates	Tracking 87952 as yet unmatched pairs. 87952 records in RAM.
INFO	2016-05-17 17:52:24	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,685
INFO	2016-05-17 17:52:24	MarkDuplicates	Tracking 25878 as yet unmatched pairs. 25878 records in RAM.
INFO	2016-05-17 17:52:33	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    8s.  Last read position: chrM:11,128
INFO	2016-05-17 17:52:33	MarkDuplicates	Tracking 68584 as yet unmatched pairs. 68584 records in RAM.
INFO	2016-05-17 17:52:36	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,352
INFO	2016-05-17 17:52:36	MarkDuplicates	Tracking 52116 as yet unmatched pairs. 52116 records in RAM.
INFO	2016-05-17 17:52:40	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,616
INFO	2016-05-17 17:52:40	MarkDuplicates	Tracking 36410 as yet unmatched pairs. 36410 records in RAM.
INFO	2016-05-17 17:52:44	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,883
INFO	2016-05-17 17:52:44	MarkDuplicates	Tracking 61198 as yet unmatched pairs. 61198 records in RAM.
INFO	2016-05-17 17:52:50	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,144
INFO	2016-05-17 17:52:50	MarkDuplicates	Tracking 63302 as yet unmatched pairs. 63302 records in RAM.
INFO	2016-05-17 17:52:53	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,536
INFO	2016-05-17 17:52:53	MarkDuplicates	Tracking 60956 as yet unmatched pairs. 60956 records in RAM.
INFO	2016-05-17 17:52:57	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,794
INFO	2016-05-17 17:52:57	MarkDuplicates	Tracking 44870 as yet unmatched pairs. 44870 records in RAM.
INFO	2016-05-17 17:53:01	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,117
INFO	2016-05-17 17:53:01	MarkDuplicates	Tracking 41794 as yet unmatched pairs. 41794 records in RAM.
INFO	2016-05-17 17:53:04	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,444
INFO	2016-05-17 17:53:04	MarkDuplicates	Tracking 39188 as yet unmatched pairs. 39188 records in RAM.
INFO	2016-05-17 17:53:08	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,848
INFO	2016-05-17 17:53:08	MarkDuplicates	Tracking 74356 as yet unmatched pairs. 74356 records in RAM.
INFO	2016-05-17 17:53:12	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,149
INFO	2016-05-17 17:53:12	MarkDuplicates	Tracking 53632 as yet unmatched pairs. 53632 records in RAM.
INFO	2016-05-17 17:53:19	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    6s.  Last read position: chrM:14,621
INFO	2016-05-17 17:53:19	MarkDuplicates	Tracking 18210 as yet unmatched pairs. 18210 records in RAM.
INFO	2016-05-17 17:53:23	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,016
INFO	2016-05-17 17:53:23	MarkDuplicates	Tracking 60106 as yet unmatched pairs. 60106 records in RAM.
INFO	2016-05-17 17:53:27	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,252
INFO	2016-05-17 17:53:27	MarkDuplicates	Tracking 60414 as yet unmatched pairs. 60414 records in RAM.
INFO	2016-05-17 17:53:43	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:   16s.  Last read position: chrM:15,511
INFO	2016-05-17 17:53:43	MarkDuplicates	Tracking 38098 as yet unmatched pairs. 38098 records in RAM.
INFO	2016-05-17 17:53:47	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,766
INFO	2016-05-17 17:53:47	MarkDuplicates	Tracking 43534 as yet unmatched pairs. 43534 records in RAM.
INFO	2016-05-17 17:53:51	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,083
INFO	2016-05-17 17:53:51	MarkDuplicates	Tracking 52350 as yet unmatched pairs. 52350 records in RAM.
INFO	2016-05-17 17:53:55	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    4s.  Last read position: chrM:16,404
INFO	2016-05-17 17:53:55	MarkDuplicates	Tracking 38278 as yet unmatched pairs. 38278 records in RAM.
INFO	2016-05-17 17:54:01	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr10:25,984,207
INFO	2016-05-17 17:54:01	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 17:54:07	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:35s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr10:95,386,678
INFO	2016-05-17 17:54:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 17:54:11	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr11:30,649,817
INFO	2016-05-17 17:54:11	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 17:54:16	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr11:96,838,463
INFO	2016-05-17 17:54:16	MarkDuplicates	Tracking 20 as yet unmatched pairs. 20 records in RAM.
INFO	2016-05-17 17:54:20	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr12:60,179,058
INFO	2016-05-17 17:54:20	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-17 17:54:24	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr13:6,689,360
INFO	2016-05-17 17:54:24	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 17:54:28	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:86,352,204
INFO	2016-05-17 17:54:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:54:32	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:56,210,411
INFO	2016-05-17 17:54:32	MarkDuplicates	Tracking 22 as yet unmatched pairs. 22 records in RAM.
INFO	2016-05-17 17:54:36	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr15:26,304,008
INFO	2016-05-17 17:54:36	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-17 17:54:43	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr15:101,858,600
INFO	2016-05-17 17:54:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 17:54:47	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:14s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr16:87,914,247
INFO	2016-05-17 17:54:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 17:54:55	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    8s.  Last read position: mm9_chr17:59,522,370
INFO	2016-05-17 17:54:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:54:59	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr18:49,892,645
INFO	2016-05-17 17:54:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:55:03	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr19:41,388,368
INFO	2016-05-17 17:55:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 17:55:07	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,618,574
INFO	2016-05-17 17:55:07	MarkDuplicates	Tracking 46430 as yet unmatched pairs. 46430 records in RAM.
INFO	2016-05-17 17:55:11	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,618,955
INFO	2016-05-17 17:55:11	MarkDuplicates	Tracking 63104 as yet unmatched pairs. 63104 records in RAM.
INFO	2016-05-17 17:55:14	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,619,316
INFO	2016-05-17 17:55:14	MarkDuplicates	Tracking 43282 as yet unmatched pairs. 43282 records in RAM.
INFO	2016-05-17 17:55:20	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr1:24,619,564
INFO	2016-05-17 17:55:20	MarkDuplicates	Tracking 185846 as yet unmatched pairs. 185846 records in RAM.
INFO	2016-05-17 17:55:25	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:24,619,888
INFO	2016-05-17 17:55:25	MarkDuplicates	Tracking 60992 as yet unmatched pairs. 60992 records in RAM.
INFO	2016-05-17 17:55:28	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,620,187
INFO	2016-05-17 17:55:28	MarkDuplicates	Tracking 41506 as yet unmatched pairs. 41506 records in RAM.
INFO	2016-05-17 17:55:32	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,620,500
INFO	2016-05-17 17:55:32	MarkDuplicates	Tracking 72208 as yet unmatched pairs. 72208 records in RAM.
INFO	2016-05-17 17:55:35	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,620,827
INFO	2016-05-17 17:55:35	MarkDuplicates	Tracking 46226 as yet unmatched pairs. 46226 records in RAM.
INFO	2016-05-17 17:55:39	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,621,182
INFO	2016-05-17 17:55:39	MarkDuplicates	Tracking 37108 as yet unmatched pairs. 37108 records in RAM.
INFO	2016-05-17 17:55:43	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:24,621,582
INFO	2016-05-17 17:55:43	MarkDuplicates	Tracking 51772 as yet unmatched pairs. 51772 records in RAM.
INFO	2016-05-17 17:55:47	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:24,621,995
INFO	2016-05-17 17:55:47	MarkDuplicates	Tracking 48162 as yet unmatched pairs. 48162 records in RAM.
INFO	2016-05-17 17:55:51	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:24,622,372
INFO	2016-05-17 17:55:51	MarkDuplicates	Tracking 37316 as yet unmatched pairs. 37316 records in RAM.
INFO	2016-05-17 17:56:09	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:   17s.  Last read position: mm9_chr1:24,622,922
INFO	2016-05-17 17:56:09	MarkDuplicates	Tracking 11010 as yet unmatched pairs. 11010 records in RAM.
INFO	2016-05-17 17:56:13	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr1:108,968,103
INFO	2016-05-17 17:56:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:56:18	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:182,906,519
INFO	2016-05-17 17:56:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:56:24	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr2:22,444,220
INFO	2016-05-17 17:56:24	MarkDuplicates	Tracking 796 as yet unmatched pairs. 796 records in RAM.
INFO	2016-05-17 17:56:29	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr2:30,273,787
INFO	2016-05-17 17:56:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:56:35	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:08:02s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr2:103,518,072
INFO	2016-05-17 17:56:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:56:41	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr2:165,231,511
INFO	2016-05-17 17:56:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:56:47	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr3:84,519,116
INFO	2016-05-17 17:56:47	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 17:56:53	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr3:149,509,556
INFO	2016-05-17 17:56:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:57:01	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:08:28s.  Time for last 1,000,000:    8s.  Last read position: mm9_chr4:83,060,428
INFO	2016-05-17 17:57:01	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 17:57:05	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr4:148,096,116
INFO	2016-05-17 17:57:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:57:09	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:08:36s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr5:76,435,904
INFO	2016-05-17 17:57:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 17:57:13	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr5:143,027,081
INFO	2016-05-17 17:57:13	MarkDuplicates	Tracking 52 as yet unmatched pairs. 52 records in RAM.
INFO	2016-05-17 17:57:17	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:80,229,017
INFO	2016-05-17 17:57:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:57:25	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr6:146,862,600
INFO	2016-05-17 17:57:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:57:29	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr7:91,033,107
INFO	2016-05-17 17:57:29	MarkDuplicates	Tracking 24 as yet unmatched pairs. 24 records in RAM.
INFO	2016-05-17 17:57:33	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr8:11,324,805
INFO	2016-05-17 17:57:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:57:37	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr8:92,671,072
INFO	2016-05-17 17:57:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:57:41	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:09:08s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr9:40,156,361
INFO	2016-05-17 17:57:41	MarkDuplicates	Tracking 46 as yet unmatched pairs. 46 records in RAM.
INFO	2016-05-17 17:57:48	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr9:107,735,337
INFO	2016-05-17 17:57:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 17:57:51	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:09:19s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:146
INFO	2016-05-17 17:57:51	MarkDuplicates	Tracking 80104 as yet unmatched pairs. 80104 records in RAM.
INFO	2016-05-17 17:57:55	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:09:22s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:353
INFO	2016-05-17 17:57:55	MarkDuplicates	Tracking 183054 as yet unmatched pairs. 183054 records in RAM.
INFO	2016-05-17 17:57:59	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:601
INFO	2016-05-17 17:57:59	MarkDuplicates	Tracking 52188 as yet unmatched pairs. 52188 records in RAM.
INFO	2016-05-17 17:58:02	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:09:30s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:811
INFO	2016-05-17 17:58:02	MarkDuplicates	Tracking 119926 as yet unmatched pairs. 119926 records in RAM.
INFO	2016-05-17 17:58:06	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,001
INFO	2016-05-17 17:58:06	MarkDuplicates	Tracking 87518 as yet unmatched pairs. 87518 records in RAM.
INFO	2016-05-17 17:58:10	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:09:37s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,199
INFO	2016-05-17 17:58:10	MarkDuplicates	Tracking 104838 as yet unmatched pairs. 104838 records in RAM.
INFO	2016-05-17 17:58:13	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,436
INFO	2016-05-17 17:58:13	MarkDuplicates	Tracking 170420 as yet unmatched pairs. 170420 records in RAM.
INFO	2016-05-17 17:58:17	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:09:44s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,673
INFO	2016-05-17 17:58:17	MarkDuplicates	Tracking 104786 as yet unmatched pairs. 104786 records in RAM.
INFO	2016-05-17 17:58:21	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:09:48s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,907
INFO	2016-05-17 17:58:21	MarkDuplicates	Tracking 71438 as yet unmatched pairs. 71438 records in RAM.
INFO	2016-05-17 17:58:39	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:10:06s.  Time for last 1,000,000:   18s.  Last read position: mm9_chrM:2,182
INFO	2016-05-17 17:58:39	MarkDuplicates	Tracking 151568 as yet unmatched pairs. 151568 records in RAM.
INFO	2016-05-17 17:58:43	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:10:10s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,494
INFO	2016-05-17 17:58:43	MarkDuplicates	Tracking 73018 as yet unmatched pairs. 73018 records in RAM.
INFO	2016-05-17 17:58:47	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:10:14s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,677
INFO	2016-05-17 17:58:47	MarkDuplicates	Tracking 151834 as yet unmatched pairs. 151834 records in RAM.
INFO	2016-05-17 17:58:52	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:2,861
INFO	2016-05-17 17:58:52	MarkDuplicates	Tracking 120330 as yet unmatched pairs. 120330 records in RAM.
INFO	2016-05-17 17:58:58	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:10:25s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:3,035
INFO	2016-05-17 17:58:58	MarkDuplicates	Tracking 127252 as yet unmatched pairs. 127252 records in RAM.
INFO	2016-05-17 17:59:03	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:3,234
INFO	2016-05-17 17:59:03	MarkDuplicates	Tracking 57932 as yet unmatched pairs. 57932 records in RAM.
INFO	2016-05-17 17:59:08	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:3,430
INFO	2016-05-17 17:59:08	MarkDuplicates	Tracking 60506 as yet unmatched pairs. 60506 records in RAM.
INFO	2016-05-17 17:59:14	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:10:41s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:3,593
INFO	2016-05-17 17:59:14	MarkDuplicates	Tracking 100934 as yet unmatched pairs. 100934 records in RAM.
INFO	2016-05-17 17:59:19	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:10:47s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:3,771
INFO	2016-05-17 17:59:19	MarkDuplicates	Tracking 110990 as yet unmatched pairs. 110990 records in RAM.
INFO	2016-05-17 17:59:27	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:10:54s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:3,955
INFO	2016-05-17 17:59:27	MarkDuplicates	Tracking 64120 as yet unmatched pairs. 64120 records in RAM.
INFO	2016-05-17 17:59:30	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:10:57s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,138
INFO	2016-05-17 17:59:30	MarkDuplicates	Tracking 102572 as yet unmatched pairs. 102572 records in RAM.
INFO	2016-05-17 17:59:34	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:11:01s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,327
INFO	2016-05-17 17:59:34	MarkDuplicates	Tracking 122592 as yet unmatched pairs. 122592 records in RAM.
INFO	2016-05-17 17:59:38	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:11:05s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,534
INFO	2016-05-17 17:59:38	MarkDuplicates	Tracking 75394 as yet unmatched pairs. 75394 records in RAM.
INFO	2016-05-17 17:59:41	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:11:08s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,706
INFO	2016-05-17 17:59:41	MarkDuplicates	Tracking 145070 as yet unmatched pairs. 145070 records in RAM.
INFO	2016-05-17 17:59:45	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:11:12s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,075
INFO	2016-05-17 17:59:45	MarkDuplicates	Tracking 100360 as yet unmatched pairs. 100360 records in RAM.
INFO	2016-05-17 17:59:53	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:11:20s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:5,324
INFO	2016-05-17 17:59:53	MarkDuplicates	Tracking 100936 as yet unmatched pairs. 100936 records in RAM.
INFO	2016-05-17 17:59:57	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:11:24s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,511
INFO	2016-05-17 17:59:57	MarkDuplicates	Tracking 130606 as yet unmatched pairs. 130606 records in RAM.
INFO	2016-05-17 18:00:01	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:11:28s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,740
INFO	2016-05-17 18:00:01	MarkDuplicates	Tracking 111050 as yet unmatched pairs. 111050 records in RAM.
INFO	2016-05-17 18:00:04	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:11:32s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,900
INFO	2016-05-17 18:00:04	MarkDuplicates	Tracking 59794 as yet unmatched pairs. 59794 records in RAM.
INFO	2016-05-17 18:00:08	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:11:35s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:6,088
INFO	2016-05-17 18:00:08	MarkDuplicates	Tracking 94300 as yet unmatched pairs. 94300 records in RAM.
INFO	2016-05-17 18:00:14	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:11:42s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:6,262
INFO	2016-05-17 18:00:14	MarkDuplicates	Tracking 90658 as yet unmatched pairs. 90658 records in RAM.
INFO	2016-05-17 18:00:18	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:11:45s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:6,512
INFO	2016-05-17 18:00:18	MarkDuplicates	Tracking 22812 as yet unmatched pairs. 22812 records in RAM.
INFO	2016-05-17 18:00:22	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:7,006
INFO	2016-05-17 18:00:22	MarkDuplicates	Tracking 25128 as yet unmatched pairs. 25128 records in RAM.
INFO	2016-05-17 18:00:25	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:11:52s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:7,371
INFO	2016-05-17 18:00:25	MarkDuplicates	Tracking 52682 as yet unmatched pairs. 52682 records in RAM.
INFO	2016-05-17 18:00:29	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:11:56s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:7,779
INFO	2016-05-17 18:00:29	MarkDuplicates	Tracking 75326 as yet unmatched pairs. 75326 records in RAM.
INFO	2016-05-17 18:00:32	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:8,194
INFO	2016-05-17 18:00:32	MarkDuplicates	Tracking 29126 as yet unmatched pairs. 29126 records in RAM.
INFO	2016-05-17 18:00:36	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:12:03s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:8,547
INFO	2016-05-17 18:00:36	MarkDuplicates	Tracking 32022 as yet unmatched pairs. 32022 records in RAM.
INFO	2016-05-17 18:00:40	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:12:07s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:8,857
INFO	2016-05-17 18:00:40	MarkDuplicates	Tracking 66612 as yet unmatched pairs. 66612 records in RAM.
INFO	2016-05-17 18:00:43	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:12:10s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:9,185
INFO	2016-05-17 18:00:43	MarkDuplicates	Tracking 40532 as yet unmatched pairs. 40532 records in RAM.
INFO	2016-05-17 18:01:01	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:12:28s.  Time for last 1,000,000:   17s.  Last read position: mm9_chrM:9,645
INFO	2016-05-17 18:01:01	MarkDuplicates	Tracking 57400 as yet unmatched pairs. 57400 records in RAM.
INFO	2016-05-17 18:01:04	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:12:32s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:10,064
INFO	2016-05-17 18:01:04	MarkDuplicates	Tracking 50242 as yet unmatched pairs. 50242 records in RAM.
INFO	2016-05-17 18:01:08	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:12:36s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:10,429
INFO	2016-05-17 18:01:08	MarkDuplicates	Tracking 56818 as yet unmatched pairs. 56818 records in RAM.
INFO	2016-05-17 18:01:13	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:12:40s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:10,809
INFO	2016-05-17 18:01:13	MarkDuplicates	Tracking 76106 as yet unmatched pairs. 76106 records in RAM.
INFO	2016-05-17 18:01:19	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:12:46s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:11,059
INFO	2016-05-17 18:01:19	MarkDuplicates	Tracking 104068 as yet unmatched pairs. 104068 records in RAM.
INFO	2016-05-17 18:01:23	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:12:50s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,219
INFO	2016-05-17 18:01:23	MarkDuplicates	Tracking 56848 as yet unmatched pairs. 56848 records in RAM.
INFO	2016-05-17 18:01:26	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,419
INFO	2016-05-17 18:01:26	MarkDuplicates	Tracking 58306 as yet unmatched pairs. 58306 records in RAM.
INFO	2016-05-17 18:01:30	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:12:57s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,620
INFO	2016-05-17 18:01:30	MarkDuplicates	Tracking 129598 as yet unmatched pairs. 129598 records in RAM.
INFO	2016-05-17 18:01:34	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:13:01s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,841
INFO	2016-05-17 18:01:34	MarkDuplicates	Tracking 100288 as yet unmatched pairs. 100288 records in RAM.
INFO	2016-05-17 18:01:37	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:13:04s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,034
INFO	2016-05-17 18:01:37	MarkDuplicates	Tracking 87738 as yet unmatched pairs. 87738 records in RAM.
INFO	2016-05-17 18:01:41	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:13:08s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,220
INFO	2016-05-17 18:01:41	MarkDuplicates	Tracking 61712 as yet unmatched pairs. 61712 records in RAM.
INFO	2016-05-17 18:01:45	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:13:12s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,419
INFO	2016-05-17 18:01:45	MarkDuplicates	Tracking 33314 as yet unmatched pairs. 33314 records in RAM.
INFO	2016-05-17 18:01:49	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:13:16s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:12,615
INFO	2016-05-17 18:01:49	MarkDuplicates	Tracking 90058 as yet unmatched pairs. 90058 records in RAM.
INFO	2016-05-17 18:01:53	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:13:20s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,799
INFO	2016-05-17 18:01:53	MarkDuplicates	Tracking 147988 as yet unmatched pairs. 147988 records in RAM.
INFO	2016-05-17 18:01:57	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:13:24s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,995
INFO	2016-05-17 18:01:57	MarkDuplicates	Tracking 63204 as yet unmatched pairs. 63204 records in RAM.
INFO	2016-05-17 18:02:06	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:13:33s.  Time for last 1,000,000:    9s.  Last read position: mm9_chrM:13,230
INFO	2016-05-17 18:02:06	MarkDuplicates	Tracking 86654 as yet unmatched pairs. 86654 records in RAM.
INFO	2016-05-17 18:02:10	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:13:37s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,439
INFO	2016-05-17 18:02:10	MarkDuplicates	Tracking 112366 as yet unmatched pairs. 112366 records in RAM.
INFO	2016-05-17 18:02:15	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:13:43s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:13,644
INFO	2016-05-17 18:02:15	MarkDuplicates	Tracking 49160 as yet unmatched pairs. 49160 records in RAM.
INFO	2016-05-17 18:02:19	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:13:46s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,859
INFO	2016-05-17 18:02:19	MarkDuplicates	Tracking 79346 as yet unmatched pairs. 79346 records in RAM.
INFO	2016-05-17 18:02:23	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:13:50s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,083
INFO	2016-05-17 18:02:23	MarkDuplicates	Tracking 145392 as yet unmatched pairs. 145392 records in RAM.
INFO	2016-05-17 18:02:26	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:13:54s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,267
INFO	2016-05-17 18:02:26	MarkDuplicates	Tracking 72506 as yet unmatched pairs. 72506 records in RAM.
INFO	2016-05-17 18:02:30	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:13:58s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,445
INFO	2016-05-17 18:02:30	MarkDuplicates	Tracking 102886 as yet unmatched pairs. 102886 records in RAM.
INFO	2016-05-17 18:02:34	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:14:01s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,609
INFO	2016-05-17 18:02:34	MarkDuplicates	Tracking 91276 as yet unmatched pairs. 91276 records in RAM.
INFO	2016-05-17 18:02:38	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:14:05s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,810
INFO	2016-05-17 18:02:38	MarkDuplicates	Tracking 99596 as yet unmatched pairs. 99596 records in RAM.
INFO	2016-05-17 18:02:41	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:14:08s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,009
INFO	2016-05-17 18:02:41	MarkDuplicates	Tracking 60166 as yet unmatched pairs. 60166 records in RAM.
INFO	2016-05-17 18:02:45	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:14:12s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,202
INFO	2016-05-17 18:02:45	MarkDuplicates	Tracking 108642 as yet unmatched pairs. 108642 records in RAM.
INFO	2016-05-17 18:02:48	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:14:16s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,382
INFO	2016-05-17 18:02:48	MarkDuplicates	Tracking 71976 as yet unmatched pairs. 71976 records in RAM.
INFO	2016-05-17 18:02:52	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:14:19s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,594
INFO	2016-05-17 18:02:52	MarkDuplicates	Tracking 65342 as yet unmatched pairs. 65342 records in RAM.
INFO	2016-05-17 18:02:56	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:14:23s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:16,242
INFO	2016-05-17 18:02:56	MarkDuplicates	Tracking 1662 as yet unmatched pairs. 1662 records in RAM.
INFO	2016-05-17 18:02:59	MarkDuplicates	Read 175770824 records. 0 pairs never matched.
INFO	2016-05-17 18:03:11	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3307025824; totalMemory: 3333947392; maxMemory: 3817865216
INFO	2016-05-17 18:03:11	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 18:03:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 18:04:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 18:05:02	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 18:05:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 3390100848; totalMemory: 3418357760; maxMemory: 3817865216
INFO	2016-05-17 18:05:03	MarkDuplicates	Marking 124769174 records as duplicates.
INFO	2016-05-17 18:05:03	MarkDuplicates	Found 38525155 optical duplicate clusters.
INFO	2016-05-17 18:06:55	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:49s.  Time for last 10,000,000:  109s.  Last read position: chr20:50,673,228
INFO	2016-05-17 18:08:56	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:50s.  Time for last 10,000,000:  121s.  Last read position: chrM:1,336
INFO	2016-05-17 18:10:44	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:38s.  Time for last 10,000,000:  107s.  Last read position: chrM:5,786
INFO	2016-05-17 18:12:32	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:26s.  Time for last 10,000,000:  108s.  Last read position: chrM:9,587
INFO	2016-05-17 18:14:20	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:09:14s.  Time for last 10,000,000:  107s.  Last read position: chrM:12,536
INFO	2016-05-17 18:16:05	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:59s.  Time for last 10,000,000:  105s.  Last read position: chrM:15,766
INFO	2016-05-17 18:18:07	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:13:01s.  Time for last 10,000,000:  121s.  Last read position: mm9_chr14:56,210,411
INFO	2016-05-17 18:20:09	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:15:03s.  Time for last 10,000,000:  122s.  Last read position: mm9_chr1:24,619,564
INFO	2016-05-17 18:21:57	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:16:51s.  Time for last 10,000,000:  108s.  Last read position: mm9_chr1:108,968,103
INFO	2016-05-17 18:24:00	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:18:54s.  Time for last 10,000,000:  122s.  Last read position: mm9_chr5:76,435,904
INFO	2016-05-17 18:26:06	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:21:00s.  Time for last 10,000,000:  126s.  Last read position: mm9_chrM:353
INFO	2016-05-17 18:27:54	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:22:48s.  Time for last 10,000,000:  108s.  Last read position: mm9_chrM:2,677
INFO	2016-05-17 18:29:40	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:24:34s.  Time for last 10,000,000:  105s.  Last read position: mm9_chrM:4,534
INFO	2016-05-17 18:31:37	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:26:31s.  Time for last 10,000,000:  117s.  Last read position: mm9_chrM:7,006
INFO	2016-05-17 18:33:24	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:28:18s.  Time for last 10,000,000:  107s.  Last read position: mm9_chrM:10,809
INFO	2016-05-17 18:35:12	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:30:06s.  Time for last 10,000,000:  107s.  Last read position: mm9_chrM:12,799
INFO	2016-05-17 18:37:03	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:31:57s.  Time for last 10,000,000:  111s.  Last read position: mm9_chrM:14,810
Could not delete file /tmp/annashch/sortingcollection.363659545317463970.tmp
Could not delete file /tmp/annashch/sortingcollection.3482292480527347769.tmp
INFO	2016-05-17 18:38:07	MarkDuplicates	Before output close freeMemory: 3480647520; totalMemory: 3511156736; maxMemory: 3817865216
INFO	2016-05-17 18:38:07	MarkDuplicates	After output close freeMemory: 3480646704; totalMemory: 3511156736; maxMemory: 3817865216
[Tue May 17 18:38:07 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 49.58 minutes.
Runtime.totalMemory()=3511156736
[bam_sort_core] merging from 72 files...

Num	5
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_10
Name	nmsrt_bam rep1
Thread	thread_20
PID	14460

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

Start	2016-05-17 11:44:44
End	2016-05-17 12:12:55
Elapsed	00:28:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

 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 325

 samtools sort -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 24 files...

Num	6
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_11
Name	bam_to_bedpe rep1
Thread	thread_20
PID	24643

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

Start	2016-05-17 12:12:55
End	2016-05-17 12:16:13
Elapsed	00:03:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep1 nmsrt_bam rep1

 
# SYS command. line 427

 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 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	7
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12
Name	bedpe_to_tag rep1
Thread	thread_20
PID	26355

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

Start	2016-05-17 12:16:15
End	2016-05-17 12:19:22
Elapsed	00:03:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 467

 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 469

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	8
ID	task.postalign_bed.spr_PE_rep1.line_248.id_13
Name	spr_PE rep1
Thread	thread_20
PID	26774

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

Start	2016-05-17 12:19:23
End	2016-05-17 12:22:15
Elapsed	00:02:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
Dependencies

 
# SYS command. line 250

 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 253

 nlines=$( zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | wc -l )

# SYS command. line 254

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

# SYS command. line 258

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.  

# SYS command. line 261

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.00" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.00

# SYS command. line 264

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.01" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz

# SYS command. line 266

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.01

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	9
ID	task.postalign_bed.shift_tag_rep1.line_140.id_14
Name	shift_tag rep1
Thread	thread_20
PID	28935

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

Start	2016-05-17 12:22:16
End	2016-05-17 12:24:01
Elapsed	00:01:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 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 144

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	10
ID	task.postalign_bed.shift_tag_rep1.line_140.id_15
Name	shift_tag rep1
Thread	thread_20
PID	28937

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

Start	2016-05-17 12:22:16
End	2016-05-17 12:23:14
Elapsed	00:00:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 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 144

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	11
ID	task.postalign_bed.shift_tag_rep1.line_140.id_16
Name	shift_tag rep1
Thread	thread_20
PID	28951

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

Start	2016-05-17 12:22:16
End	2016-05-17 12:23:14
Elapsed	00:00:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 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 144

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	12
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_17
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	29172

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

Start	2016-05-17 12:24:02
End	2016-05-17 12:25:38
Elapsed	00:01:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

 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 95

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	13
ID	task.postalign_bed.xcor_rep1.line_165.id_18
Name	xcor rep1
Thread	thread_20
PID	30799

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

Start	2016-05-17 12:25:39
End	2016-05-17 13:02:36
Elapsed	00:36:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpKESP2e/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign78fa1422898c
done. read 25000000 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1406617 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.225303890715891 
Top 3 estimates for fragment length 0 
Window half size 430 
Phantom peak location 80 
Phantom peak Correlation 0.245046 
Normalized Strand cross-correlation coefficient (NSC) 1.601743 
Relative Strand Cross correlation Coefficient (RSC) 0.8108709 
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

Num	14
ID	task.callpeak_macs2.macs2_atac_rep1_pr1.pval0.1.line_192.id_19
Name	macs2_atac rep1-pr1.pval0.1
Thread	thread_20
PID	30801

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

Start	2016-05-17 12:25:39
End	2016-05-17 12:40:51
Elapsed	00:15:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 12:25:42: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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-01
# 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 12:25:42: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:25:42: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:25:44:  1000000 
INFO  @ Tue, 17 May 2016 12:25:46:  2000000 
INFO  @ Tue, 17 May 2016 12:25:48:  3000000 
INFO  @ Tue, 17 May 2016 12:25:50:  4000000 
INFO  @ Tue, 17 May 2016 12:25:52:  5000000 
INFO  @ Tue, 17 May 2016 12:25:54:  6000000 
INFO  @ Tue, 17 May 2016 12:25:56:  7000000 
INFO  @ Tue, 17 May 2016 12:25:58:  8000000 
INFO  @ Tue, 17 May 2016 12:26:00:  9000000 
INFO  @ Tue, 17 May 2016 12:26:02:  10000000 
INFO  @ Tue, 17 May 2016 12:26:04:  11000000 
INFO  @ Tue, 17 May 2016 12:26:07:  12000000 
INFO  @ Tue, 17 May 2016 12:26:09:  13000000 
INFO  @ Tue, 17 May 2016 12:26:11:  14000000 
INFO  @ Tue, 17 May 2016 12:26:13:  15000000 
INFO  @ Tue, 17 May 2016 12:26:15:  16000000 
INFO  @ Tue, 17 May 2016 12:26:17:  17000000 
INFO  @ Tue, 17 May 2016 12:26:19:  18000000 
INFO  @ Tue, 17 May 2016 12:26:21:  19000000 
INFO  @ Tue, 17 May 2016 12:26:23:  20000000 
INFO  @ Tue, 17 May 2016 12:26:25:  21000000 
INFO  @ Tue, 17 May 2016 12:26:27:  22000000 
INFO  @ Tue, 17 May 2016 12:26:29:  23000000 
INFO  @ Tue, 17 May 2016 12:26:31:  24000000 
INFO  @ Tue, 17 May 2016 12:26:33:  25000000 
INFO  @ Tue, 17 May 2016 12:26:35:  26000000 
INFO  @ Tue, 17 May 2016 12:26:37:  27000000 
INFO  @ Tue, 17 May 2016 12:26:39:  28000000 
INFO  @ Tue, 17 May 2016 12:26:41:  29000000 
INFO  @ Tue, 17 May 2016 12:26:43: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 12:26:43: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 12:26:43: #1  total tags in treatment: 29044156 
INFO  @ Tue, 17 May 2016 12:26:43: #1 finished! 
INFO  @ Tue, 17 May 2016 12:26:43: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:26:43: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:26:43: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:26:43: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:26:43: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:26:43: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 12:26:43: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:28:10: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:30:09: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 12:30:13: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 12:30:15: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 12:30:18: Done! 
INFO  @ Tue, 17 May 2016 12:30:29: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 12:30:29: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:30:29: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:30:31:  1000000 
INFO  @ Tue, 17 May 2016 12:30:33:  2000000 
INFO  @ Tue, 17 May 2016 12:30:35:  3000000 
INFO  @ Tue, 17 May 2016 12:30:37:  4000000 
INFO  @ Tue, 17 May 2016 12:30:39:  5000000 
INFO  @ Tue, 17 May 2016 12:30:41:  6000000 
INFO  @ Tue, 17 May 2016 12:30:43:  7000000 
INFO  @ Tue, 17 May 2016 12:30:45:  8000000 
INFO  @ Tue, 17 May 2016 12:30:47:  9000000 
INFO  @ Tue, 17 May 2016 12:30:49:  10000000 
INFO  @ Tue, 17 May 2016 12:30:51:  11000000 
INFO  @ Tue, 17 May 2016 12:30:52:  12000000 
INFO  @ Tue, 17 May 2016 12:30:54:  13000000 
INFO  @ Tue, 17 May 2016 12:30:56:  14000000 
INFO  @ Tue, 17 May 2016 12:30:58:  15000000 
INFO  @ Tue, 17 May 2016 12:31:00:  16000000 
INFO  @ Tue, 17 May 2016 12:31:02:  17000000 
INFO  @ Tue, 17 May 2016 12:31:04:  18000000 
INFO  @ Tue, 17 May 2016 12:31:06:  19000000 
INFO  @ Tue, 17 May 2016 12:31:08:  20000000 
INFO  @ Tue, 17 May 2016 12:31:10:  21000000 
INFO  @ Tue, 17 May 2016 12:31:12:  22000000 
INFO  @ Tue, 17 May 2016 12:31:14:  23000000 
INFO  @ Tue, 17 May 2016 12:31:16:  24000000 
INFO  @ Tue, 17 May 2016 12:31:18:  25000000 
INFO  @ Tue, 17 May 2016 12:31:20:  26000000 
INFO  @ Tue, 17 May 2016 12:31:22:  27000000 
INFO  @ Tue, 17 May 2016 12:31:24:  28000000 
INFO  @ Tue, 17 May 2016 12:31:26:  29000000 
INFO  @ Tue, 17 May 2016 12:31:28: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 12:31:28: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 12:31:28: #1  total tags in treatment: 29044156 
INFO  @ Tue, 17 May 2016 12:31:28: #1 finished! 
INFO  @ Tue, 17 May 2016 12:31:28: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:31:28: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:31:28: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:31:28: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:31:28: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:31:28: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 12:31:28: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 12:31:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:32:56: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 12:32:56: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 12:32:56: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 12:32:56: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 12:32:56: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:40:32: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 12:40:39: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 12:40:44: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 12:40:47: Done!

Num	15
ID	task.callpeak_macs2.macs2_atac_rep1_pr2.pval0.1.line_192.id_20
Name	macs2_atac rep1-pr2.pval0.1
Thread	thread_20
PID	30811

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

Start	2016-05-17 12:25:39
End	2016-05-17 12:40:14
Elapsed	00:14:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 12:25:42: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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-01
# 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 12:25:42: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:25:42: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:25:44:  1000000 
INFO  @ Tue, 17 May 2016 12:25:46:  2000000 
INFO  @ Tue, 17 May 2016 12:25:48:  3000000 
INFO  @ Tue, 17 May 2016 12:25:50:  4000000 
INFO  @ Tue, 17 May 2016 12:25:52:  5000000 
INFO  @ Tue, 17 May 2016 12:25:54:  6000000 
INFO  @ Tue, 17 May 2016 12:25:56:  7000000 
INFO  @ Tue, 17 May 2016 12:25:58:  8000000 
INFO  @ Tue, 17 May 2016 12:26:00:  9000000 
INFO  @ Tue, 17 May 2016 12:26:02:  10000000 
INFO  @ Tue, 17 May 2016 12:26:04:  11000000 
INFO  @ Tue, 17 May 2016 12:26:06:  12000000 
INFO  @ Tue, 17 May 2016 12:26:08:  13000000 
INFO  @ Tue, 17 May 2016 12:26:10:  14000000 
INFO  @ Tue, 17 May 2016 12:26:12:  15000000 
INFO  @ Tue, 17 May 2016 12:26:14:  16000000 
INFO  @ Tue, 17 May 2016 12:26:16:  17000000 
INFO  @ Tue, 17 May 2016 12:26:18:  18000000 
INFO  @ Tue, 17 May 2016 12:26:20:  19000000 
INFO  @ Tue, 17 May 2016 12:26:21:  20000000 
INFO  @ Tue, 17 May 2016 12:26:23:  21000000 
INFO  @ Tue, 17 May 2016 12:26:25:  22000000 
INFO  @ Tue, 17 May 2016 12:26:27:  23000000 
INFO  @ Tue, 17 May 2016 12:26:29:  24000000 
INFO  @ Tue, 17 May 2016 12:26:32:  25000000 
INFO  @ Tue, 17 May 2016 12:26:33:  26000000 
INFO  @ Tue, 17 May 2016 12:26:35:  27000000 
INFO  @ Tue, 17 May 2016 12:26:37:  28000000 
INFO  @ Tue, 17 May 2016 12:26:39:  29000000 
INFO  @ Tue, 17 May 2016 12:26:42: #1 tag size is determined as 55 bps 
INFO  @ Tue, 17 May 2016 12:26:42: #1 tag size = 55 
INFO  @ Tue, 17 May 2016 12:26:42: #1  total tags in treatment: 29044156 
INFO  @ Tue, 17 May 2016 12:26:42: #1 finished! 
INFO  @ Tue, 17 May 2016 12:26:42: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:26:42: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:26:42: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:26:42: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:26:42: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:26:42: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 12:26:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:28:05: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:29:57: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 12:30:00: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 12:30:03: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 12:30:05: Done! 
INFO  @ Tue, 17 May 2016 12:30:16: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 12:30:16: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:30:16: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:30:18:  1000000 
INFO  @ Tue, 17 May 2016 12:30:20:  2000000 
INFO  @ Tue, 17 May 2016 12:30:22:  3000000 
INFO  @ Tue, 17 May 2016 12:30:24:  4000000 
INFO  @ Tue, 17 May 2016 12:30:26:  5000000 
INFO  @ Tue, 17 May 2016 12:30:28:  6000000 
INFO  @ Tue, 17 May 2016 12:30:30:  7000000 
INFO  @ Tue, 17 May 2016 12:30:32:  8000000 
INFO  @ Tue, 17 May 2016 12:30:34:  9000000 
INFO  @ Tue, 17 May 2016 12:30:36:  10000000 
INFO  @ Tue, 17 May 2016 12:30:38:  11000000 
INFO  @ Tue, 17 May 2016 12:30:40:  12000000 
INFO  @ Tue, 17 May 2016 12:30:42:  13000000 
INFO  @ Tue, 17 May 2016 12:30:44:  14000000 
INFO  @ Tue, 17 May 2016 12:30:45:  15000000 
INFO  @ Tue, 17 May 2016 12:30:47:  16000000 
INFO  @ Tue, 17 May 2016 12:30:49:  17000000 
INFO  @ Tue, 17 May 2016 12:30:51:  18000000 
INFO  @ Tue, 17 May 2016 12:30:53:  19000000 
INFO  @ Tue, 17 May 2016 12:30:55:  20000000 
INFO  @ Tue, 17 May 2016 12:30:57:  21000000 
INFO  @ Tue, 17 May 2016 12:30:59:  22000000 
INFO  @ Tue, 17 May 2016 12:31:01:  23000000 
INFO  @ Tue, 17 May 2016 12:31:03:  24000000 
INFO  @ Tue, 17 May 2016 12:31:05:  25000000 
INFO  @ Tue, 17 May 2016 12:31:06:  26000000 
INFO  @ Tue, 17 May 2016 12:31:08:  27000000 
INFO  @ Tue, 17 May 2016 12:31:10:  28000000 
INFO  @ Tue, 17 May 2016 12:31:12:  29000000 
INFO  @ Tue, 17 May 2016 12:31:14: #1 tag size is determined as 55 bps 
INFO  @ Tue, 17 May 2016 12:31:14: #1 tag size = 55 
INFO  @ Tue, 17 May 2016 12:31:14: #1  total tags in treatment: 29044156 
INFO  @ Tue, 17 May 2016 12:31:14: #1 finished! 
INFO  @ Tue, 17 May 2016 12:31:14: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:31:14: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:31:14: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:31:14: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:31:14: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:31:14: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 12:31:14: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 12:31:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:32:39: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 12:32:39: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 12:32:39: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 12:32:39: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 12:32:39: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:39:56: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 12:40:02: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 12:40:06: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 12:40:09: Done!

Num	16
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_21
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	36482

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

Start	2016-05-17 12:40:52
End	2016-05-17 13:02:05
Elapsed	00:21:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 12:40:55: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_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-01
# 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 12:40:55: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:40:55: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:40:57:  1000000 
INFO  @ Tue, 17 May 2016 12:40:59:  2000000 
INFO  @ Tue, 17 May 2016 12:41:01:  3000000 
INFO  @ Tue, 17 May 2016 12:41:03:  4000000 
INFO  @ Tue, 17 May 2016 12:41:05:  5000000 
INFO  @ Tue, 17 May 2016 12:41:07:  6000000 
INFO  @ Tue, 17 May 2016 12:41:09:  7000000 
INFO  @ Tue, 17 May 2016 12:41:11:  8000000 
INFO  @ Tue, 17 May 2016 12:41:12:  9000000 
INFO  @ Tue, 17 May 2016 12:41:14:  10000000 
INFO  @ Tue, 17 May 2016 12:41:16:  11000000 
INFO  @ Tue, 17 May 2016 12:41:18:  12000000 
INFO  @ Tue, 17 May 2016 12:41:20:  13000000 
INFO  @ Tue, 17 May 2016 12:41:22:  14000000 
INFO  @ Tue, 17 May 2016 12:41:24:  15000000 
INFO  @ Tue, 17 May 2016 12:41:26:  16000000 
INFO  @ Tue, 17 May 2016 12:41:28:  17000000 
INFO  @ Tue, 17 May 2016 12:41:30:  18000000 
INFO  @ Tue, 17 May 2016 12:41:32:  19000000 
INFO  @ Tue, 17 May 2016 12:41:34:  20000000 
INFO  @ Tue, 17 May 2016 12:41:36:  21000000 
INFO  @ Tue, 17 May 2016 12:41:38:  22000000 
INFO  @ Tue, 17 May 2016 12:41:40:  23000000 
INFO  @ Tue, 17 May 2016 12:41:42:  24000000 
INFO  @ Tue, 17 May 2016 12:41:44:  25000000 
INFO  @ Tue, 17 May 2016 12:41:46:  26000000 
INFO  @ Tue, 17 May 2016 12:41:48:  27000000 
INFO  @ Tue, 17 May 2016 12:41:50:  28000000 
INFO  @ Tue, 17 May 2016 12:41:52:  29000000 
INFO  @ Tue, 17 May 2016 12:41:53:  30000000 
INFO  @ Tue, 17 May 2016 12:41:55:  31000000 
INFO  @ Tue, 17 May 2016 12:41:57:  32000000 
INFO  @ Tue, 17 May 2016 12:41:59:  33000000 
INFO  @ Tue, 17 May 2016 12:42:01:  34000000 
INFO  @ Tue, 17 May 2016 12:42:03:  35000000 
INFO  @ Tue, 17 May 2016 12:42:05:  36000000 
INFO  @ Tue, 17 May 2016 12:42:07:  37000000 
INFO  @ Tue, 17 May 2016 12:42:09:  38000000 
INFO  @ Tue, 17 May 2016 12:42:11:  39000000 
INFO  @ Tue, 17 May 2016 12:42:13:  40000000 
INFO  @ Tue, 17 May 2016 12:42:15:  41000000 
INFO  @ Tue, 17 May 2016 12:42:17:  42000000 
INFO  @ Tue, 17 May 2016 12:42:19:  43000000 
INFO  @ Tue, 17 May 2016 12:42:21:  44000000 
INFO  @ Tue, 17 May 2016 12:42:23:  45000000 
INFO  @ Tue, 17 May 2016 12:42:25:  46000000 
INFO  @ Tue, 17 May 2016 12:42:27:  47000000 
INFO  @ Tue, 17 May 2016 12:42:29:  48000000 
INFO  @ Tue, 17 May 2016 12:42:31:  49000000 
INFO  @ Tue, 17 May 2016 12:42:32:  50000000 
INFO  @ Tue, 17 May 2016 12:42:34:  51000000 
INFO  @ Tue, 17 May 2016 12:42:36:  52000000 
INFO  @ Tue, 17 May 2016 12:42:42: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 12:42:42: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 12:42:42: #1  total tags in treatment: 52988292 
INFO  @ Tue, 17 May 2016 12:42:42: #1 finished! 
INFO  @ Tue, 17 May 2016 12:42:42: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:42:42: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:42:42: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:42:42: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:42:42: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:42:42: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 12:42:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:44:51: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:47:54: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 12:47:58: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 12:48:00: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 12:48:02: Done! 
INFO  @ Tue, 17 May 2016 12:48:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_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-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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 12:48:12: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:48:12: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:48:14:  1000000 
INFO  @ Tue, 17 May 2016 12:48:16:  2000000 
INFO  @ Tue, 17 May 2016 12:48:18:  3000000 
INFO  @ Tue, 17 May 2016 12:48:21:  4000000 
INFO  @ Tue, 17 May 2016 12:48:23:  5000000 
INFO  @ Tue, 17 May 2016 12:48:25:  6000000 
INFO  @ Tue, 17 May 2016 12:48:27:  7000000 
INFO  @ Tue, 17 May 2016 12:48:29:  8000000 
INFO  @ Tue, 17 May 2016 12:48:31:  9000000 
INFO  @ Tue, 17 May 2016 12:48:33:  10000000 
INFO  @ Tue, 17 May 2016 12:48:35:  11000000 
INFO  @ Tue, 17 May 2016 12:48:37:  12000000 
INFO  @ Tue, 17 May 2016 12:48:39:  13000000 
INFO  @ Tue, 17 May 2016 12:48:41:  14000000 
INFO  @ Tue, 17 May 2016 12:48:43:  15000000 
INFO  @ Tue, 17 May 2016 12:48:45:  16000000 
INFO  @ Tue, 17 May 2016 12:48:47:  17000000 
INFO  @ Tue, 17 May 2016 12:48:49:  18000000 
INFO  @ Tue, 17 May 2016 12:48:51:  19000000 
INFO  @ Tue, 17 May 2016 12:48:53:  20000000 
INFO  @ Tue, 17 May 2016 12:48:55:  21000000 
INFO  @ Tue, 17 May 2016 12:48:57:  22000000 
INFO  @ Tue, 17 May 2016 12:48:59:  23000000 
INFO  @ Tue, 17 May 2016 12:49:01:  24000000 
INFO  @ Tue, 17 May 2016 12:49:03:  25000000 
INFO  @ Tue, 17 May 2016 12:49:05:  26000000 
INFO  @ Tue, 17 May 2016 12:49:07:  27000000 
INFO  @ Tue, 17 May 2016 12:49:09:  28000000 
INFO  @ Tue, 17 May 2016 12:49:11:  29000000 
INFO  @ Tue, 17 May 2016 12:49:13:  30000000 
INFO  @ Tue, 17 May 2016 12:49:15:  31000000 
INFO  @ Tue, 17 May 2016 12:49:18:  32000000 
INFO  @ Tue, 17 May 2016 12:49:20:  33000000 
INFO  @ Tue, 17 May 2016 12:49:22:  34000000 
INFO  @ Tue, 17 May 2016 12:49:24:  35000000 
INFO  @ Tue, 17 May 2016 12:49:26:  36000000 
INFO  @ Tue, 17 May 2016 12:49:28:  37000000 
INFO  @ Tue, 17 May 2016 12:49:30:  38000000 
INFO  @ Tue, 17 May 2016 12:49:32:  39000000 
INFO  @ Tue, 17 May 2016 12:49:34:  40000000 
INFO  @ Tue, 17 May 2016 12:49:36:  41000000 
INFO  @ Tue, 17 May 2016 12:49:38:  42000000 
INFO  @ Tue, 17 May 2016 12:49:40:  43000000 
INFO  @ Tue, 17 May 2016 12:49:42:  44000000 
INFO  @ Tue, 17 May 2016 12:49:44:  45000000 
INFO  @ Tue, 17 May 2016 12:49:46:  46000000 
INFO  @ Tue, 17 May 2016 12:49:48:  47000000 
INFO  @ Tue, 17 May 2016 12:49:50:  48000000 
INFO  @ Tue, 17 May 2016 12:49:52:  49000000 
INFO  @ Tue, 17 May 2016 12:49:54:  50000000 
INFO  @ Tue, 17 May 2016 12:49:56:  51000000 
INFO  @ Tue, 17 May 2016 12:49:58:  52000000 
INFO  @ Tue, 17 May 2016 12:50:05: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 12:50:05: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 12:50:05: #1  total tags in treatment: 52988292 
INFO  @ Tue, 17 May 2016 12:50:05: #1 finished! 
INFO  @ Tue, 17 May 2016 12:50:05: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:50:05: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:50:05: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:50:05: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:50:05: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:50:05: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 12:50:05: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 12:50:05: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:52:13: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 12:52:13: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 12:52:13: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 12:52:13: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 12:52:13: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 13:01:47: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 13:01:54: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 13:01:58: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 13:02:00: Done!

Num	17
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_22
Name	macs2_atac rep1
Thread	thread_20
PID	36487

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

Start	2016-05-17 12:40:52
End	2016-05-17 13:43:57
Elapsed	01:03:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_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_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_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_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_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 12:40:55: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_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 12:40:55: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:40:55: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:40:57:  1000000 
INFO  @ Tue, 17 May 2016 12:40:59:  2000000 
INFO  @ Tue, 17 May 2016 12:41:01:  3000000 
INFO  @ Tue, 17 May 2016 12:41:04:  4000000 
INFO  @ Tue, 17 May 2016 12:41:06:  5000000 
INFO  @ Tue, 17 May 2016 12:41:08:  6000000 
INFO  @ Tue, 17 May 2016 12:41:10:  7000000 
INFO  @ Tue, 17 May 2016 12:41:12:  8000000 
INFO  @ Tue, 17 May 2016 12:41:14:  9000000 
INFO  @ Tue, 17 May 2016 12:41:16:  10000000 
INFO  @ Tue, 17 May 2016 12:41:19:  11000000 
INFO  @ Tue, 17 May 2016 12:41:21:  12000000 
INFO  @ Tue, 17 May 2016 12:41:23:  13000000 
INFO  @ Tue, 17 May 2016 12:41:25:  14000000 
INFO  @ Tue, 17 May 2016 12:41:27:  15000000 
INFO  @ Tue, 17 May 2016 12:41:29:  16000000 
INFO  @ Tue, 17 May 2016 12:41:32:  17000000 
INFO  @ Tue, 17 May 2016 12:41:34:  18000000 
INFO  @ Tue, 17 May 2016 12:41:36:  19000000 
INFO  @ Tue, 17 May 2016 12:41:38:  20000000 
INFO  @ Tue, 17 May 2016 12:41:40:  21000000 
INFO  @ Tue, 17 May 2016 12:41:42:  22000000 
INFO  @ Tue, 17 May 2016 12:41:44:  23000000 
INFO  @ Tue, 17 May 2016 12:41:47:  24000000 
INFO  @ Tue, 17 May 2016 12:41:49:  25000000 
INFO  @ Tue, 17 May 2016 12:41:51:  26000000 
INFO  @ Tue, 17 May 2016 12:41:53:  27000000 
INFO  @ Tue, 17 May 2016 12:41:55:  28000000 
INFO  @ Tue, 17 May 2016 12:41:57:  29000000 
INFO  @ Tue, 17 May 2016 12:42:00:  30000000 
INFO  @ Tue, 17 May 2016 12:42:02:  31000000 
INFO  @ Tue, 17 May 2016 12:42:04:  32000000 
INFO  @ Tue, 17 May 2016 12:42:06:  33000000 
INFO  @ Tue, 17 May 2016 12:42:08:  34000000 
INFO  @ Tue, 17 May 2016 12:42:10:  35000000 
INFO  @ Tue, 17 May 2016 12:42:12:  36000000 
INFO  @ Tue, 17 May 2016 12:42:14:  37000000 
INFO  @ Tue, 17 May 2016 12:42:16:  38000000 
INFO  @ Tue, 17 May 2016 12:42:18:  39000000 
INFO  @ Tue, 17 May 2016 12:42:21:  40000000 
INFO  @ Tue, 17 May 2016 12:42:23:  41000000 
INFO  @ Tue, 17 May 2016 12:42:25:  42000000 
INFO  @ Tue, 17 May 2016 12:42:27:  43000000 
INFO  @ Tue, 17 May 2016 12:42:29:  44000000 
INFO  @ Tue, 17 May 2016 12:42:31:  45000000 
INFO  @ Tue, 17 May 2016 12:42:33:  46000000 
INFO  @ Tue, 17 May 2016 12:42:35:  47000000 
INFO  @ Tue, 17 May 2016 12:42:37:  48000000 
INFO  @ Tue, 17 May 2016 12:42:39:  49000000 
INFO  @ Tue, 17 May 2016 12:42:41:  50000000 
INFO  @ Tue, 17 May 2016 12:42:43:  51000000 
INFO  @ Tue, 17 May 2016 12:42:45:  52000000 
INFO  @ Tue, 17 May 2016 12:42:52: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 12:42:52: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 12:42:52: #1  total tags in treatment: 52988292 
INFO  @ Tue, 17 May 2016 12:42:52: #1 finished! 
INFO  @ Tue, 17 May 2016 12:42:52: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:42:52: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:42:52: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:42:52: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:42:52: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:42:52: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 12:42:52: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:45:00: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:47:37: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 12:47:40: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 12:47:42: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 12:47:45: Done! 
INFO  @ Tue, 17 May 2016 12:47:55: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_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 12:47:55: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:47:55: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:47:57:  1000000 
INFO  @ Tue, 17 May 2016 12:47:59:  2000000 
INFO  @ Tue, 17 May 2016 12:48:01:  3000000 
INFO  @ Tue, 17 May 2016 12:48:03:  4000000 
INFO  @ Tue, 17 May 2016 12:48:05:  5000000 
INFO  @ Tue, 17 May 2016 12:48:07:  6000000 
INFO  @ Tue, 17 May 2016 12:48:09:  7000000 
INFO  @ Tue, 17 May 2016 12:48:11:  8000000 
INFO  @ Tue, 17 May 2016 12:48:13:  9000000 
INFO  @ Tue, 17 May 2016 12:48:15:  10000000 
INFO  @ Tue, 17 May 2016 12:48:17:  11000000 
INFO  @ Tue, 17 May 2016 12:48:19:  12000000 
INFO  @ Tue, 17 May 2016 12:48:21:  13000000 
INFO  @ Tue, 17 May 2016 12:48:23:  14000000 
INFO  @ Tue, 17 May 2016 12:48:25:  15000000 
INFO  @ Tue, 17 May 2016 12:48:27:  16000000 
INFO  @ Tue, 17 May 2016 12:48:29:  17000000 
INFO  @ Tue, 17 May 2016 12:48:31:  18000000 
INFO  @ Tue, 17 May 2016 12:48:33:  19000000 
INFO  @ Tue, 17 May 2016 12:48:35:  20000000 
INFO  @ Tue, 17 May 2016 12:48:37:  21000000 
INFO  @ Tue, 17 May 2016 12:48:39:  22000000 
INFO  @ Tue, 17 May 2016 12:48:41:  23000000 
INFO  @ Tue, 17 May 2016 12:48:43:  24000000 
INFO  @ Tue, 17 May 2016 12:48:45:  25000000 
INFO  @ Tue, 17 May 2016 12:48:47:  26000000 
INFO  @ Tue, 17 May 2016 12:48:49:  27000000 
INFO  @ Tue, 17 May 2016 12:48:51:  28000000 
INFO  @ Tue, 17 May 2016 12:48:53:  29000000 
INFO  @ Tue, 17 May 2016 12:48:55:  30000000 
INFO  @ Tue, 17 May 2016 12:48:57:  31000000 
INFO  @ Tue, 17 May 2016 12:48:59:  32000000 
INFO  @ Tue, 17 May 2016 12:49:01:  33000000 
INFO  @ Tue, 17 May 2016 12:49:03:  34000000 
INFO  @ Tue, 17 May 2016 12:49:05:  35000000 
INFO  @ Tue, 17 May 2016 12:49:06:  36000000 
INFO  @ Tue, 17 May 2016 12:49:08:  37000000 
INFO  @ Tue, 17 May 2016 12:49:10:  38000000 
INFO  @ Tue, 17 May 2016 12:49:12:  39000000 
INFO  @ Tue, 17 May 2016 12:49:14:  40000000 
INFO  @ Tue, 17 May 2016 12:49:16:  41000000 
INFO  @ Tue, 17 May 2016 12:49:18:  42000000 
INFO  @ Tue, 17 May 2016 12:49:20:  43000000 
INFO  @ Tue, 17 May 2016 12:49:22:  44000000 
INFO  @ Tue, 17 May 2016 12:49:25:  45000000 
INFO  @ Tue, 17 May 2016 12:49:26:  46000000 
INFO  @ Tue, 17 May 2016 12:49:29:  47000000 
INFO  @ Tue, 17 May 2016 12:49:31:  48000000 
INFO  @ Tue, 17 May 2016 12:49:33:  49000000 
INFO  @ Tue, 17 May 2016 12:49:35:  50000000 
INFO  @ Tue, 17 May 2016 12:49:37:  51000000 
INFO  @ Tue, 17 May 2016 12:49:39:  52000000 
INFO  @ Tue, 17 May 2016 12:49:45: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 12:49:45: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 12:49:45: #1  total tags in treatment: 52988292 
INFO  @ Tue, 17 May 2016 12:49:45: #1 finished! 
INFO  @ Tue, 17 May 2016 12:49:45: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:49:45: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:49:45: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:49:45: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:49:45: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:49:45: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 12:49:45: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 12:49:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:51:54: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 12:51:54: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 12:51:54: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 12:51:54: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 12:51:54: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:59:13: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 12:59:17: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 12:59:19: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 12:59:20: Done! 
INFO  @ Tue, 17 May 2016 12:59:24: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 13:01:16: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 13:01:54: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 13:02:33: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 13:08:25: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 13:11:44: Finished 'FE'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 13:22:48: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 13:24:35: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 13:25:12: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 13:25:50: Values in your input bedGraph files will be multiplied by 52.988292 ... 
INFO  @ Tue, 17 May 2016 13:31:36: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 13:32:54: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 13:35:28: Finished 'ppois'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_ppois.bdg'!

Num	18
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_23
Name	nmsrt_bam rep2
Thread	thread_21
PID	38237

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

Start	2016-05-17 20:42:46
End	2016-05-17 21:12:39
Elapsed	00:29:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

 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 325

 samtools sort -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 21 files...

Num	19
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_24
Name	bam_to_bedpe rep2
Thread	thread_21
PID	402

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

Start	2016-05-17 21:12:39
End	2016-05-17 21:16:07
Elapsed	00:03:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep2 nmsrt_bam rep2

 
# SYS command. line 427

 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 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	20
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_25
Name	bedpe_to_tag rep2
Thread	thread_21
PID	2116

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

Start	2016-05-17 21:16:09
End	2016-05-17 21:18:50
Elapsed	00:02:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 467

 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 469

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	21
ID	task.postalign_bed.spr_PE_rep2.line_248.id_26
Name	spr_PE rep2
Thread	thread_21
PID	2219

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

Start	2016-05-17 21:18:51
End	2016-05-17 21:22:27
Elapsed	00:03:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
Dependencies

 
# SYS command. line 250

 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 253

 nlines=$( zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | wc -l )

# SYS command. line 254

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

# SYS command. line 258

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.  

# SYS command. line 261

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.00" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.00

# SYS command. line 264

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.01" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz

# SYS command. line 266

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.01

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	22
ID	task.postalign_bed.shift_tag_rep2.line_140.id_27
Name	shift_tag rep2
Thread	thread_21
PID	4000

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

Start	2016-05-17 21:22:27
End	2016-05-17 21:24:01
Elapsed	00:01:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 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 144

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	23
ID	task.postalign_bed.shift_tag_rep2.line_140.id_28
Name	shift_tag rep2
Thread	thread_21
PID	4004

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

Start	2016-05-17 21:22:27
End	2016-05-17 21:23:44
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 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 144

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	24
ID	task.postalign_bed.shift_tag_rep2.line_140.id_29
Name	shift_tag rep2
Thread	thread_21
PID	4021

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

Start	2016-05-17 21:22:28
End	2016-05-17 21:23:43
Elapsed	00:01:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 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 144

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	25
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_30
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	4194

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

Start	2016-05-17 21:24:02
End	2016-05-17 21:26:21
Elapsed	00:02:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

 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 95

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	26
ID	task.postalign_bed.xcor_rep2.line_165.id_31
Name	xcor rep2
Thread	thread_21
PID	5841

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

Start	2016-05-17 21:26:22
End	2016-05-17 22:02:03
Elapsed	00:35:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/annashch/output/4x_experiments/baseChroms_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpkZ8s10/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign177b5e75dc04
done. read 22199272 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1295303 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.241591915808267 
Top 3 estimates for fragment length 0 
Window half size 500 
Phantom peak location 80 
Phantom peak Correlation 0.2619588 
Normalized Strand cross-correlation coefficient (NSC) 1.865139 
Relative Strand Cross correlation Coefficient (RSC) 0.846205 
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

Num	27
ID	task.callpeak_macs2.macs2_atac_rep2_pr1.pval0.1.line_192.id_32
Name	macs2_atac rep2-pr1.pval0.1
Thread	thread_21
PID	5843

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

Start	2016-05-17 21:26:22
End	2016-05-17 21:43:08
Elapsed	00:16:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 21:26:27: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.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-01
# 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 21:26:27: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:26:27: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:26:29:  1000000 
INFO  @ Tue, 17 May 2016 21:26:31:  2000000 
INFO  @ Tue, 17 May 2016 21:26:33:  3000000 
INFO  @ Tue, 17 May 2016 21:26:36:  4000000 
INFO  @ Tue, 17 May 2016 21:26:38:  5000000 
INFO  @ Tue, 17 May 2016 21:26:40:  6000000 
INFO  @ Tue, 17 May 2016 21:26:42:  7000000 
INFO  @ Tue, 17 May 2016 21:26:44:  8000000 
INFO  @ Tue, 17 May 2016 21:26:46:  9000000 
INFO  @ Tue, 17 May 2016 21:26:48:  10000000 
INFO  @ Tue, 17 May 2016 21:26:51:  11000000 
INFO  @ Tue, 17 May 2016 21:26:54:  12000000 
INFO  @ Tue, 17 May 2016 21:26:56:  13000000 
INFO  @ Tue, 17 May 2016 21:26:58:  14000000 
INFO  @ Tue, 17 May 2016 21:27:00:  15000000 
INFO  @ Tue, 17 May 2016 21:27:02:  16000000 
INFO  @ Tue, 17 May 2016 21:27:05:  17000000 
INFO  @ Tue, 17 May 2016 21:27:07:  18000000 
INFO  @ Tue, 17 May 2016 21:27:09:  19000000 
INFO  @ Tue, 17 May 2016 21:27:11:  20000000 
INFO  @ Tue, 17 May 2016 21:27:14:  21000000 
INFO  @ Tue, 17 May 2016 21:27:16:  22000000 
INFO  @ Tue, 17 May 2016 21:27:18:  23000000 
INFO  @ Tue, 17 May 2016 21:27:20:  24000000 
INFO  @ Tue, 17 May 2016 21:27:22:  25000000 
INFO  @ Tue, 17 May 2016 21:27:26: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 21:27:26: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 21:27:26: #1  total tags in treatment: 25500826 
INFO  @ Tue, 17 May 2016 21:27:26: #1 finished! 
INFO  @ Tue, 17 May 2016 21:27:26: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:27:26: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:27:26: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:27:26: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:27:26: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:27:26: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 21:27:26: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:29:33: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 21:32:15: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 21:32:18: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 21:32:21: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 21:32:23: Done! 
INFO  @ Tue, 17 May 2016 21:32:41: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 21:32:41: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:32:41: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:32:43:  1000000 
INFO  @ Tue, 17 May 2016 21:32:47:  2000000 
INFO  @ Tue, 17 May 2016 21:32:50:  3000000 
INFO  @ Tue, 17 May 2016 21:32:52:  4000000 
INFO  @ Tue, 17 May 2016 21:32:55:  5000000 
INFO  @ Tue, 17 May 2016 21:32:58:  6000000 
INFO  @ Tue, 17 May 2016 21:33:00:  7000000 
INFO  @ Tue, 17 May 2016 21:33:04:  8000000 
INFO  @ Tue, 17 May 2016 21:33:07:  9000000 
INFO  @ Tue, 17 May 2016 21:33:10:  10000000 
INFO  @ Tue, 17 May 2016 21:33:12:  11000000 
INFO  @ Tue, 17 May 2016 21:33:15:  12000000 
INFO  @ Tue, 17 May 2016 21:33:19:  13000000 
INFO  @ Tue, 17 May 2016 21:33:22:  14000000 
INFO  @ Tue, 17 May 2016 21:33:25:  15000000 
INFO  @ Tue, 17 May 2016 21:33:29:  16000000 
INFO  @ Tue, 17 May 2016 21:33:32:  17000000 
INFO  @ Tue, 17 May 2016 21:33:35:  18000000 
INFO  @ Tue, 17 May 2016 21:33:37:  19000000 
INFO  @ Tue, 17 May 2016 21:33:39:  20000000 
INFO  @ Tue, 17 May 2016 21:33:42:  21000000 
INFO  @ Tue, 17 May 2016 21:33:44:  22000000 
INFO  @ Tue, 17 May 2016 21:33:47:  23000000 
INFO  @ Tue, 17 May 2016 21:33:49:  24000000 
INFO  @ Tue, 17 May 2016 21:33:51:  25000000 
INFO  @ Tue, 17 May 2016 21:33:55: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 21:33:55: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 21:33:55: #1  total tags in treatment: 25500826 
INFO  @ Tue, 17 May 2016 21:33:55: #1 finished! 
INFO  @ Tue, 17 May 2016 21:33:55: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:33:55: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:33:55: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:33:55: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:33:55: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:33:55: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 21:33:55: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 21:33:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:36:02: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 21:36:02: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 21:36:02: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 21:36:02: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 21:36:02: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 21:42:50: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 21:42:55: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 21:42:58: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 21:43:00: Done!

Num	28
ID	task.callpeak_macs2.macs2_atac_rep2_pr2.pval0.1.line_192.id_33
Name	macs2_atac rep2-pr2.pval0.1
Thread	thread_21
PID	5861

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

Start	2016-05-17 21:26:22
End	2016-05-17 21:41:58
Elapsed	00:15:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 21:26:27: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.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-01
# 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 21:26:27: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:26:27: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:26:29:  1000000 
INFO  @ Tue, 17 May 2016 21:26:31:  2000000 
INFO  @ Tue, 17 May 2016 21:26:33:  3000000 
INFO  @ Tue, 17 May 2016 21:26:35:  4000000 
INFO  @ Tue, 17 May 2016 21:26:37:  5000000 
INFO  @ Tue, 17 May 2016 21:26:39:  6000000 
INFO  @ Tue, 17 May 2016 21:26:41:  7000000 
INFO  @ Tue, 17 May 2016 21:26:43:  8000000 
INFO  @ Tue, 17 May 2016 21:26:46:  9000000 
INFO  @ Tue, 17 May 2016 21:26:48:  10000000 
INFO  @ Tue, 17 May 2016 21:26:50:  11000000 
INFO  @ Tue, 17 May 2016 21:26:52:  12000000 
INFO  @ Tue, 17 May 2016 21:26:54:  13000000 
INFO  @ Tue, 17 May 2016 21:26:56:  14000000 
INFO  @ Tue, 17 May 2016 21:26:58:  15000000 
INFO  @ Tue, 17 May 2016 21:27:00:  16000000 
INFO  @ Tue, 17 May 2016 21:27:02:  17000000 
INFO  @ Tue, 17 May 2016 21:27:04:  18000000 
INFO  @ Tue, 17 May 2016 21:27:06:  19000000 
INFO  @ Tue, 17 May 2016 21:27:08:  20000000 
INFO  @ Tue, 17 May 2016 21:27:10:  21000000 
INFO  @ Tue, 17 May 2016 21:27:12:  22000000 
INFO  @ Tue, 17 May 2016 21:27:14:  23000000 
INFO  @ Tue, 17 May 2016 21:27:16:  24000000 
INFO  @ Tue, 17 May 2016 21:27:19:  25000000 
INFO  @ Tue, 17 May 2016 21:27:22: #1 tag size is determined as 53 bps 
INFO  @ Tue, 17 May 2016 21:27:22: #1 tag size = 53 
INFO  @ Tue, 17 May 2016 21:27:22: #1  total tags in treatment: 25500824 
INFO  @ Tue, 17 May 2016 21:27:22: #1 finished! 
INFO  @ Tue, 17 May 2016 21:27:22: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:27:22: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:27:22: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:27:22: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:27:22: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:27:22: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 21:27:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:29:03: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 21:30:53: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 21:30:57: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 21:30:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 21:31:01: Done! 
INFO  @ Tue, 17 May 2016 21:31:20: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 21:31:20: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:31:20: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:31:23:  1000000 
INFO  @ Tue, 17 May 2016 21:31:26:  2000000 
INFO  @ Tue, 17 May 2016 21:31:29:  3000000 
INFO  @ Tue, 17 May 2016 21:31:32:  4000000 
INFO  @ Tue, 17 May 2016 21:31:34:  5000000 
INFO  @ Tue, 17 May 2016 21:31:37:  6000000 
INFO  @ Tue, 17 May 2016 21:31:39:  7000000 
INFO  @ Tue, 17 May 2016 21:31:42:  8000000 
INFO  @ Tue, 17 May 2016 21:31:45:  9000000 
INFO  @ Tue, 17 May 2016 21:31:47:  10000000 
INFO  @ Tue, 17 May 2016 21:31:50:  11000000 
INFO  @ Tue, 17 May 2016 21:31:53:  12000000 
INFO  @ Tue, 17 May 2016 21:31:56:  13000000 
INFO  @ Tue, 17 May 2016 21:31:59:  14000000 
INFO  @ Tue, 17 May 2016 21:32:02:  15000000 
INFO  @ Tue, 17 May 2016 21:32:05:  16000000 
INFO  @ Tue, 17 May 2016 21:32:08:  17000000 
INFO  @ Tue, 17 May 2016 21:32:11:  18000000 
INFO  @ Tue, 17 May 2016 21:32:14:  19000000 
INFO  @ Tue, 17 May 2016 21:32:17:  20000000 
INFO  @ Tue, 17 May 2016 21:32:19:  21000000 
INFO  @ Tue, 17 May 2016 21:32:22:  22000000 
INFO  @ Tue, 17 May 2016 21:32:25:  23000000 
INFO  @ Tue, 17 May 2016 21:32:28:  24000000 
INFO  @ Tue, 17 May 2016 21:32:31:  25000000 
INFO  @ Tue, 17 May 2016 21:32:34: #1 tag size is determined as 53 bps 
INFO  @ Tue, 17 May 2016 21:32:34: #1 tag size = 53 
INFO  @ Tue, 17 May 2016 21:32:34: #1  total tags in treatment: 25500824 
INFO  @ Tue, 17 May 2016 21:32:34: #1 finished! 
INFO  @ Tue, 17 May 2016 21:32:34: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:32:34: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:32:34: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:32:34: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:32:34: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:32:34: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 21:32:34: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 21:32:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:34:40: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 21:34:40: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 21:34:40: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 21:34:40: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 21:34:40: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 21:41:40: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 21:41:44: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 21:41:48: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 21:41:50: Done!

Num	29
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_34
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	11118

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

Start	2016-05-17 21:43:09
End	2016-05-17 22:03:31
Elapsed	00:20:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 21:43:14: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_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-01
# 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 21:43:14: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:43:14: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:43:16:  1000000 
INFO  @ Tue, 17 May 2016 21:43:18:  2000000 
INFO  @ Tue, 17 May 2016 21:43:20:  3000000 
INFO  @ Tue, 17 May 2016 21:43:22:  4000000 
INFO  @ Tue, 17 May 2016 21:43:25:  5000000 
INFO  @ Tue, 17 May 2016 21:43:27:  6000000 
INFO  @ Tue, 17 May 2016 21:43:29:  7000000 
INFO  @ Tue, 17 May 2016 21:43:31:  8000000 
INFO  @ Tue, 17 May 2016 21:43:34:  9000000 
INFO  @ Tue, 17 May 2016 21:43:36:  10000000 
INFO  @ Tue, 17 May 2016 21:43:38:  11000000 
INFO  @ Tue, 17 May 2016 21:43:40:  12000000 
INFO  @ Tue, 17 May 2016 21:43:43:  13000000 
INFO  @ Tue, 17 May 2016 21:43:46:  14000000 
INFO  @ Tue, 17 May 2016 21:43:48:  15000000 
INFO  @ Tue, 17 May 2016 21:43:51:  16000000 
INFO  @ Tue, 17 May 2016 21:43:54:  17000000 
INFO  @ Tue, 17 May 2016 21:43:56:  18000000 
INFO  @ Tue, 17 May 2016 21:43:58:  19000000 
INFO  @ Tue, 17 May 2016 21:44:00:  20000000 
INFO  @ Tue, 17 May 2016 21:44:02:  21000000 
INFO  @ Tue, 17 May 2016 21:44:04:  22000000 
INFO  @ Tue, 17 May 2016 21:44:06:  23000000 
INFO  @ Tue, 17 May 2016 21:44:08:  24000000 
INFO  @ Tue, 17 May 2016 21:44:10:  25000000 
INFO  @ Tue, 17 May 2016 21:44:13:  26000000 
INFO  @ Tue, 17 May 2016 21:44:15:  27000000 
INFO  @ Tue, 17 May 2016 21:44:18:  28000000 
INFO  @ Tue, 17 May 2016 21:44:20:  29000000 
INFO  @ Tue, 17 May 2016 21:44:22:  30000000 
INFO  @ Tue, 17 May 2016 21:44:24:  31000000 
INFO  @ Tue, 17 May 2016 21:44:27:  32000000 
INFO  @ Tue, 17 May 2016 21:44:29:  33000000 
INFO  @ Tue, 17 May 2016 21:44:31:  34000000 
INFO  @ Tue, 17 May 2016 21:44:33:  35000000 
INFO  @ Tue, 17 May 2016 21:44:35:  36000000 
INFO  @ Tue, 17 May 2016 21:44:37:  37000000 
INFO  @ Tue, 17 May 2016 21:44:40:  38000000 
INFO  @ Tue, 17 May 2016 21:44:42:  39000000 
INFO  @ Tue, 17 May 2016 21:44:44:  40000000 
INFO  @ Tue, 17 May 2016 21:44:46:  41000000 
INFO  @ Tue, 17 May 2016 21:44:48:  42000000 
INFO  @ Tue, 17 May 2016 21:44:50:  43000000 
INFO  @ Tue, 17 May 2016 21:44:52:  44000000 
INFO  @ Tue, 17 May 2016 21:44:57: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 21:44:57: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 21:44:57: #1  total tags in treatment: 44398544 
INFO  @ Tue, 17 May 2016 21:44:57: #1 finished! 
INFO  @ Tue, 17 May 2016 21:44:57: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:44:57: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:44:57: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:44:57: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:44:57: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:44:57: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 21:44:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:47:37: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 21:50:36: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 21:50:39: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 21:50:41: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 21:50:42: Done! 
INFO  @ Tue, 17 May 2016 21:50:55: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_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-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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 21:50:55: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:50:55: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:50:57:  1000000 
INFO  @ Tue, 17 May 2016 21:50:59:  2000000 
INFO  @ Tue, 17 May 2016 21:51:02:  3000000 
INFO  @ Tue, 17 May 2016 21:51:04:  4000000 
INFO  @ Tue, 17 May 2016 21:51:06:  5000000 
INFO  @ Tue, 17 May 2016 21:51:08:  6000000 
INFO  @ Tue, 17 May 2016 21:51:10:  7000000 
INFO  @ Tue, 17 May 2016 21:51:12:  8000000 
INFO  @ Tue, 17 May 2016 21:51:14:  9000000 
INFO  @ Tue, 17 May 2016 21:51:16:  10000000 
INFO  @ Tue, 17 May 2016 21:51:18:  11000000 
INFO  @ Tue, 17 May 2016 21:51:20:  12000000 
INFO  @ Tue, 17 May 2016 21:51:22:  13000000 
INFO  @ Tue, 17 May 2016 21:51:24:  14000000 
INFO  @ Tue, 17 May 2016 21:51:26:  15000000 
INFO  @ Tue, 17 May 2016 21:51:29:  16000000 
INFO  @ Tue, 17 May 2016 21:51:31:  17000000 
INFO  @ Tue, 17 May 2016 21:51:33:  18000000 
INFO  @ Tue, 17 May 2016 21:51:35:  19000000 
INFO  @ Tue, 17 May 2016 21:51:37:  20000000 
INFO  @ Tue, 17 May 2016 21:51:39:  21000000 
INFO  @ Tue, 17 May 2016 21:51:41:  22000000 
INFO  @ Tue, 17 May 2016 21:51:43:  23000000 
INFO  @ Tue, 17 May 2016 21:51:46:  24000000 
INFO  @ Tue, 17 May 2016 21:51:48:  25000000 
INFO  @ Tue, 17 May 2016 21:51:50:  26000000 
INFO  @ Tue, 17 May 2016 21:51:52:  27000000 
INFO  @ Tue, 17 May 2016 21:51:54:  28000000 
INFO  @ Tue, 17 May 2016 21:51:56:  29000000 
INFO  @ Tue, 17 May 2016 21:51:58:  30000000 
INFO  @ Tue, 17 May 2016 21:52:00:  31000000 
INFO  @ Tue, 17 May 2016 21:52:02:  32000000 
INFO  @ Tue, 17 May 2016 21:52:05:  33000000 
INFO  @ Tue, 17 May 2016 21:52:07:  34000000 
INFO  @ Tue, 17 May 2016 21:52:09:  35000000 
INFO  @ Tue, 17 May 2016 21:52:11:  36000000 
INFO  @ Tue, 17 May 2016 21:52:13:  37000000 
INFO  @ Tue, 17 May 2016 21:52:15:  38000000 
INFO  @ Tue, 17 May 2016 21:52:17:  39000000 
INFO  @ Tue, 17 May 2016 21:52:19:  40000000 
INFO  @ Tue, 17 May 2016 21:52:21:  41000000 
INFO  @ Tue, 17 May 2016 21:52:23:  42000000 
INFO  @ Tue, 17 May 2016 21:52:25:  43000000 
INFO  @ Tue, 17 May 2016 21:52:27:  44000000 
INFO  @ Tue, 17 May 2016 21:52:32: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 21:52:32: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 21:52:32: #1  total tags in treatment: 44398544 
INFO  @ Tue, 17 May 2016 21:52:32: #1 finished! 
INFO  @ Tue, 17 May 2016 21:52:32: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:52:32: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:52:32: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:52:32: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:52:32: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:52:32: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 21:52:32: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 21:52:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:55:12: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 21:55:12: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 21:55:12: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 21:55:12: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 21:55:12: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 22:03:14: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 22:03:19: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 22:03:22: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 22:03:24: Done!

Num	30
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_35
Name	macs2_atac rep2
Thread	thread_21
PID	11123

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

Start	2016-05-17 21:43:09
End	2016-05-17 22:37:57
Elapsed	00:54:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_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/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_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 21:43:14: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_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 21:43:14: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:43:14: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:43:17:  1000000 
INFO  @ Tue, 17 May 2016 21:43:19:  2000000 
INFO  @ Tue, 17 May 2016 21:43:21:  3000000 
INFO  @ Tue, 17 May 2016 21:43:23:  4000000 
INFO  @ Tue, 17 May 2016 21:43:26:  5000000 
INFO  @ Tue, 17 May 2016 21:43:28:  6000000 
INFO  @ Tue, 17 May 2016 21:43:31:  7000000 
INFO  @ Tue, 17 May 2016 21:43:33:  8000000 
INFO  @ Tue, 17 May 2016 21:43:35:  9000000 
INFO  @ Tue, 17 May 2016 21:43:37:  10000000 
INFO  @ Tue, 17 May 2016 21:43:39:  11000000 
INFO  @ Tue, 17 May 2016 21:43:41:  12000000 
INFO  @ Tue, 17 May 2016 21:43:43:  13000000 
INFO  @ Tue, 17 May 2016 21:43:45:  14000000 
INFO  @ Tue, 17 May 2016 21:43:47:  15000000 
INFO  @ Tue, 17 May 2016 21:43:49:  16000000 
INFO  @ Tue, 17 May 2016 21:43:51:  17000000 
INFO  @ Tue, 17 May 2016 21:43:53:  18000000 
INFO  @ Tue, 17 May 2016 21:43:55:  19000000 
INFO  @ Tue, 17 May 2016 21:43:57:  20000000 
INFO  @ Tue, 17 May 2016 21:43:59:  21000000 
INFO  @ Tue, 17 May 2016 21:44:01:  22000000 
INFO  @ Tue, 17 May 2016 21:44:03:  23000000 
INFO  @ Tue, 17 May 2016 21:44:05:  24000000 
INFO  @ Tue, 17 May 2016 21:44:07:  25000000 
INFO  @ Tue, 17 May 2016 21:44:09:  26000000 
INFO  @ Tue, 17 May 2016 21:44:12:  27000000 
INFO  @ Tue, 17 May 2016 21:44:14:  28000000 
INFO  @ Tue, 17 May 2016 21:44:16:  29000000 
INFO  @ Tue, 17 May 2016 21:44:18:  30000000 
INFO  @ Tue, 17 May 2016 21:44:20:  31000000 
INFO  @ Tue, 17 May 2016 21:44:22:  32000000 
INFO  @ Tue, 17 May 2016 21:44:24:  33000000 
INFO  @ Tue, 17 May 2016 21:44:26:  34000000 
INFO  @ Tue, 17 May 2016 21:44:28:  35000000 
INFO  @ Tue, 17 May 2016 21:44:30:  36000000 
INFO  @ Tue, 17 May 2016 21:44:32:  37000000 
INFO  @ Tue, 17 May 2016 21:44:34:  38000000 
INFO  @ Tue, 17 May 2016 21:44:36:  39000000 
INFO  @ Tue, 17 May 2016 21:44:38:  40000000 
INFO  @ Tue, 17 May 2016 21:44:40:  41000000 
INFO  @ Tue, 17 May 2016 21:44:42:  42000000 
INFO  @ Tue, 17 May 2016 21:44:44:  43000000 
INFO  @ Tue, 17 May 2016 21:44:46:  44000000 
INFO  @ Tue, 17 May 2016 21:44:51: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 21:44:51: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 21:44:51: #1  total tags in treatment: 44398544 
INFO  @ Tue, 17 May 2016 21:44:51: #1 finished! 
INFO  @ Tue, 17 May 2016 21:44:51: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:44:51: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:44:51: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:44:51: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:44:51: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:44:51: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 21:44:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:47:31: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 21:50:17: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 21:50:19: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 21:50:21: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 21:50:23: Done! 
INFO  @ Tue, 17 May 2016 21:50:35: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_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 21:50:35: #1 read tag files... 
INFO  @ Tue, 17 May 2016 21:50:35: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 21:50:38:  1000000 
INFO  @ Tue, 17 May 2016 21:50:40:  2000000 
INFO  @ Tue, 17 May 2016 21:50:42:  3000000 
INFO  @ Tue, 17 May 2016 21:50:44:  4000000 
INFO  @ Tue, 17 May 2016 21:50:46:  5000000 
INFO  @ Tue, 17 May 2016 21:50:48:  6000000 
INFO  @ Tue, 17 May 2016 21:50:50:  7000000 
INFO  @ Tue, 17 May 2016 21:50:52:  8000000 
INFO  @ Tue, 17 May 2016 21:50:54:  9000000 
INFO  @ Tue, 17 May 2016 21:50:56:  10000000 
INFO  @ Tue, 17 May 2016 21:50:58:  11000000 
INFO  @ Tue, 17 May 2016 21:51:00:  12000000 
INFO  @ Tue, 17 May 2016 21:51:02:  13000000 
INFO  @ Tue, 17 May 2016 21:51:04:  14000000 
INFO  @ Tue, 17 May 2016 21:51:06:  15000000 
INFO  @ Tue, 17 May 2016 21:51:08:  16000000 
INFO  @ Tue, 17 May 2016 21:51:10:  17000000 
INFO  @ Tue, 17 May 2016 21:51:13:  18000000 
INFO  @ Tue, 17 May 2016 21:51:15:  19000000 
INFO  @ Tue, 17 May 2016 21:51:17:  20000000 
INFO  @ Tue, 17 May 2016 21:51:19:  21000000 
INFO  @ Tue, 17 May 2016 21:51:21:  22000000 
INFO  @ Tue, 17 May 2016 21:51:23:  23000000 
INFO  @ Tue, 17 May 2016 21:51:25:  24000000 
INFO  @ Tue, 17 May 2016 21:51:27:  25000000 
INFO  @ Tue, 17 May 2016 21:51:29:  26000000 
INFO  @ Tue, 17 May 2016 21:51:31:  27000000 
INFO  @ Tue, 17 May 2016 21:51:33:  28000000 
INFO  @ Tue, 17 May 2016 21:51:35:  29000000 
INFO  @ Tue, 17 May 2016 21:51:37:  30000000 
INFO  @ Tue, 17 May 2016 21:51:39:  31000000 
INFO  @ Tue, 17 May 2016 21:51:41:  32000000 
INFO  @ Tue, 17 May 2016 21:51:43:  33000000 
INFO  @ Tue, 17 May 2016 21:51:46:  34000000 
INFO  @ Tue, 17 May 2016 21:51:48:  35000000 
INFO  @ Tue, 17 May 2016 21:51:50:  36000000 
INFO  @ Tue, 17 May 2016 21:51:52:  37000000 
INFO  @ Tue, 17 May 2016 21:51:54:  38000000 
INFO  @ Tue, 17 May 2016 21:51:56:  39000000 
INFO  @ Tue, 17 May 2016 21:51:58:  40000000 
INFO  @ Tue, 17 May 2016 21:52:00:  41000000 
INFO  @ Tue, 17 May 2016 21:52:02:  42000000 
INFO  @ Tue, 17 May 2016 21:52:04:  43000000 
INFO  @ Tue, 17 May 2016 21:52:06:  44000000 
INFO  @ Tue, 17 May 2016 21:52:10: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 21:52:10: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 21:52:10: #1  total tags in treatment: 44398544 
INFO  @ Tue, 17 May 2016 21:52:10: #1 finished! 
INFO  @ Tue, 17 May 2016 21:52:10: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 21:52:10: #2 Skipped... 
INFO  @ Tue, 17 May 2016 21:52:10: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 21:52:10: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 21:52:10: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 21:52:10: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 21:52:10: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 21:52:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 21:54:46: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 21:54:46: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 21:54:46: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 21:54:46: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 21:54:46: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 22:01:45: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 22:01:48: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 22:01:50: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 22:01:51: Done! 
INFO  @ Tue, 17 May 2016 22:01:59: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 22:03:33: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 22:04:12: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 22:05:08: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 22:09:26: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 22:12:04: Finished 'FE'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 22:19:51: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 22:21:30: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 22:22:08: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 22:23:09: Values in your input bedGraph files will be multiplied by 44.398544 ... 
INFO  @ Tue, 17 May 2016 22:28:17: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 22:29:41: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 22:31:39: Finished 'ppois'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_ppois.bdg'!

Num	31
ID	task.postalign_bed.pool_tag_reps.line_405.id_36
Name	pool_tag reps
Thread	thread_Root
PID	30137

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

Start	2016-05-17 22:37:58
End	2016-05-17 22:40:42
Elapsed	00:02:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz
Dependencies

 
# SYS command. line 407

 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 408

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz  | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	32
ID	task.postalign_bed.pool_tag_reps_pr1.line_405.id_37
Name	pool_tag reps-pr1
Thread	thread_Root
PID	30139

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

Start	2016-05-17 22:37:58
End	2016-05-17 22:39:29
Elapsed	00:01:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz
Dependencies

 
# SYS command. line 407

 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 408

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz  | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	33
ID	task.postalign_bed.pool_tag_reps_pr2.line_405.id_38
Name	pool_tag reps-pr2
Thread	thread_Root
PID	30148

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

Start	2016-05-17 22:37:58
End	2016-05-17 22:39:30
Elapsed	00:01:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz
Dependencies

 
# SYS command. line 407

 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 408

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz  | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	34
ID	task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_39
Name	macs2_atac pooled.pval0.1
Thread	thread_Root
PID	31899

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

Start	2016-05-17 22:40:43
End	2016-05-17 23:16:01
Elapsed	00:35:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 22:40:45: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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-01
# 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 22:40:45: #1 read tag files... 
INFO  @ Tue, 17 May 2016 22:40:45: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 22:40:47:  1000000 
INFO  @ Tue, 17 May 2016 22:40:50:  2000000 
INFO  @ Tue, 17 May 2016 22:40:52:  3000000 
INFO  @ Tue, 17 May 2016 22:40:54:  4000000 
INFO  @ Tue, 17 May 2016 22:40:56:  5000000 
INFO  @ Tue, 17 May 2016 22:40:58:  6000000 
INFO  @ Tue, 17 May 2016 22:41:00:  7000000 
INFO  @ Tue, 17 May 2016 22:41:02:  8000000 
INFO  @ Tue, 17 May 2016 22:41:04:  9000000 
INFO  @ Tue, 17 May 2016 22:41:06:  10000000 
INFO  @ Tue, 17 May 2016 22:41:08:  11000000 
INFO  @ Tue, 17 May 2016 22:41:10:  12000000 
INFO  @ Tue, 17 May 2016 22:41:12:  13000000 
INFO  @ Tue, 17 May 2016 22:41:14:  14000000 
INFO  @ Tue, 17 May 2016 22:41:16:  15000000 
INFO  @ Tue, 17 May 2016 22:41:18:  16000000 
INFO  @ Tue, 17 May 2016 22:41:20:  17000000 
INFO  @ Tue, 17 May 2016 22:41:23:  18000000 
INFO  @ Tue, 17 May 2016 22:41:25:  19000000 
INFO  @ Tue, 17 May 2016 22:41:27:  20000000 
INFO  @ Tue, 17 May 2016 22:41:29:  21000000 
INFO  @ Tue, 17 May 2016 22:41:31:  22000000 
INFO  @ Tue, 17 May 2016 22:41:33:  23000000 
INFO  @ Tue, 17 May 2016 22:41:35:  24000000 
INFO  @ Tue, 17 May 2016 22:41:37:  25000000 
INFO  @ Tue, 17 May 2016 22:41:39:  26000000 
INFO  @ Tue, 17 May 2016 22:41:41:  27000000 
INFO  @ Tue, 17 May 2016 22:41:43:  28000000 
INFO  @ Tue, 17 May 2016 22:41:45:  29000000 
INFO  @ Tue, 17 May 2016 22:41:47:  30000000 
INFO  @ Tue, 17 May 2016 22:41:49:  31000000 
INFO  @ Tue, 17 May 2016 22:41:51:  32000000 
INFO  @ Tue, 17 May 2016 22:41:53:  33000000 
INFO  @ Tue, 17 May 2016 22:41:55:  34000000 
INFO  @ Tue, 17 May 2016 22:41:58:  35000000 
INFO  @ Tue, 17 May 2016 22:42:00:  36000000 
INFO  @ Tue, 17 May 2016 22:42:02:  37000000 
INFO  @ Tue, 17 May 2016 22:42:04:  38000000 
INFO  @ Tue, 17 May 2016 22:42:06:  39000000 
INFO  @ Tue, 17 May 2016 22:42:08:  40000000 
INFO  @ Tue, 17 May 2016 22:42:10:  41000000 
INFO  @ Tue, 17 May 2016 22:42:12:  42000000 
INFO  @ Tue, 17 May 2016 22:42:14:  43000000 
INFO  @ Tue, 17 May 2016 22:42:16:  44000000 
INFO  @ Tue, 17 May 2016 22:42:18:  45000000 
INFO  @ Tue, 17 May 2016 22:42:20:  46000000 
INFO  @ Tue, 17 May 2016 22:42:22:  47000000 
INFO  @ Tue, 17 May 2016 22:42:24:  48000000 
INFO  @ Tue, 17 May 2016 22:42:26:  49000000 
INFO  @ Tue, 17 May 2016 22:42:28:  50000000 
INFO  @ Tue, 17 May 2016 22:42:30:  51000000 
INFO  @ Tue, 17 May 2016 22:42:33:  52000000 
INFO  @ Tue, 17 May 2016 22:42:35:  53000000 
INFO  @ Tue, 17 May 2016 22:42:37:  54000000 
INFO  @ Tue, 17 May 2016 22:42:39:  55000000 
INFO  @ Tue, 17 May 2016 22:42:41:  56000000 
INFO  @ Tue, 17 May 2016 22:42:43:  57000000 
INFO  @ Tue, 17 May 2016 22:42:45:  58000000 
INFO  @ Tue, 17 May 2016 22:42:47:  59000000 
INFO  @ Tue, 17 May 2016 22:42:49:  60000000 
INFO  @ Tue, 17 May 2016 22:42:51:  61000000 
INFO  @ Tue, 17 May 2016 22:42:53:  62000000 
INFO  @ Tue, 17 May 2016 22:42:55:  63000000 
INFO  @ Tue, 17 May 2016 22:42:57:  64000000 
INFO  @ Tue, 17 May 2016 22:42:59:  65000000 
INFO  @ Tue, 17 May 2016 22:43:01:  66000000 
INFO  @ Tue, 17 May 2016 22:43:03:  67000000 
INFO  @ Tue, 17 May 2016 22:43:05:  68000000 
INFO  @ Tue, 17 May 2016 22:43:07:  69000000 
INFO  @ Tue, 17 May 2016 22:43:09:  70000000 
INFO  @ Tue, 17 May 2016 22:43:11:  71000000 
INFO  @ Tue, 17 May 2016 22:43:13:  72000000 
INFO  @ Tue, 17 May 2016 22:43:15:  73000000 
INFO  @ Tue, 17 May 2016 22:43:17:  74000000 
INFO  @ Tue, 17 May 2016 22:43:19:  75000000 
INFO  @ Tue, 17 May 2016 22:43:21:  76000000 
INFO  @ Tue, 17 May 2016 22:43:23:  77000000 
INFO  @ Tue, 17 May 2016 22:43:25:  78000000 
INFO  @ Tue, 17 May 2016 22:43:27:  79000000 
INFO  @ Tue, 17 May 2016 22:43:29:  80000000 
INFO  @ Tue, 17 May 2016 22:43:32:  81000000 
INFO  @ Tue, 17 May 2016 22:43:35:  82000000 
INFO  @ Tue, 17 May 2016 22:43:39:  83000000 
INFO  @ Tue, 17 May 2016 22:43:42:  84000000 
INFO  @ Tue, 17 May 2016 22:43:45:  85000000 
INFO  @ Tue, 17 May 2016 22:43:49:  86000000 
INFO  @ Tue, 17 May 2016 22:43:51:  87000000 
INFO  @ Tue, 17 May 2016 22:43:54:  88000000 
INFO  @ Tue, 17 May 2016 22:43:56:  89000000 
INFO  @ Tue, 17 May 2016 22:44:00:  90000000 
INFO  @ Tue, 17 May 2016 22:44:03:  91000000 
INFO  @ Tue, 17 May 2016 22:44:06:  92000000 
INFO  @ Tue, 17 May 2016 22:44:09:  93000000 
INFO  @ Tue, 17 May 2016 22:44:12:  94000000 
INFO  @ Tue, 17 May 2016 22:44:15:  95000000 
INFO  @ Tue, 17 May 2016 22:44:18:  96000000 
INFO  @ Tue, 17 May 2016 22:44:21:  97000000 
INFO  @ Tue, 17 May 2016 22:44:31: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 22:44:31: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 22:44:31: #1  total tags in treatment: 97386836 
INFO  @ Tue, 17 May 2016 22:44:31: #1 finished! 
INFO  @ Tue, 17 May 2016 22:44:31: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 22:44:31: #2 Skipped... 
INFO  @ Tue, 17 May 2016 22:44:31: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 22:44:31: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 22:44:31: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 22:44:31: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 22:44:31: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 22:49:39: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 22:54:26: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 22:54:30: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 22:54:32: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 22:54:34: Done! 
INFO  @ Tue, 17 May 2016 22:54:44: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 22:54:44: #1 read tag files... 
INFO  @ Tue, 17 May 2016 22:54:44: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 22:54:46:  1000000 
INFO  @ Tue, 17 May 2016 22:54:48:  2000000 
INFO  @ Tue, 17 May 2016 22:54:50:  3000000 
INFO  @ Tue, 17 May 2016 22:54:52:  4000000 
INFO  @ Tue, 17 May 2016 22:54:54:  5000000 
INFO  @ Tue, 17 May 2016 22:54:56:  6000000 
INFO  @ Tue, 17 May 2016 22:54:58:  7000000 
INFO  @ Tue, 17 May 2016 22:55:00:  8000000 
INFO  @ Tue, 17 May 2016 22:55:03:  9000000 
INFO  @ Tue, 17 May 2016 22:55:05:  10000000 
INFO  @ Tue, 17 May 2016 22:55:07:  11000000 
INFO  @ Tue, 17 May 2016 22:55:09:  12000000 
INFO  @ Tue, 17 May 2016 22:55:11:  13000000 
INFO  @ Tue, 17 May 2016 22:55:13:  14000000 
INFO  @ Tue, 17 May 2016 22:55:16:  15000000 
INFO  @ Tue, 17 May 2016 22:55:18:  16000000 
INFO  @ Tue, 17 May 2016 22:55:20:  17000000 
INFO  @ Tue, 17 May 2016 22:55:22:  18000000 
INFO  @ Tue, 17 May 2016 22:55:24:  19000000 
INFO  @ Tue, 17 May 2016 22:55:26:  20000000 
INFO  @ Tue, 17 May 2016 22:55:28:  21000000 
INFO  @ Tue, 17 May 2016 22:55:30:  22000000 
INFO  @ Tue, 17 May 2016 22:55:32:  23000000 
INFO  @ Tue, 17 May 2016 22:55:35:  24000000 
INFO  @ Tue, 17 May 2016 22:55:37:  25000000 
INFO  @ Tue, 17 May 2016 22:55:39:  26000000 
INFO  @ Tue, 17 May 2016 22:55:41:  27000000 
INFO  @ Tue, 17 May 2016 22:55:43:  28000000 
INFO  @ Tue, 17 May 2016 22:55:45:  29000000 
INFO  @ Tue, 17 May 2016 22:55:47:  30000000 
INFO  @ Tue, 17 May 2016 22:55:49:  31000000 
INFO  @ Tue, 17 May 2016 22:55:51:  32000000 
INFO  @ Tue, 17 May 2016 22:55:53:  33000000 
INFO  @ Tue, 17 May 2016 22:55:55:  34000000 
INFO  @ Tue, 17 May 2016 22:55:57:  35000000 
INFO  @ Tue, 17 May 2016 22:56:00:  36000000 
INFO  @ Tue, 17 May 2016 22:56:02:  37000000 
INFO  @ Tue, 17 May 2016 22:56:04:  38000000 
INFO  @ Tue, 17 May 2016 22:56:06:  39000000 
INFO  @ Tue, 17 May 2016 22:56:08:  40000000 
INFO  @ Tue, 17 May 2016 22:56:10:  41000000 
INFO  @ Tue, 17 May 2016 22:56:12:  42000000 
INFO  @ Tue, 17 May 2016 22:56:14:  43000000 
INFO  @ Tue, 17 May 2016 22:56:16:  44000000 
INFO  @ Tue, 17 May 2016 22:56:18:  45000000 
INFO  @ Tue, 17 May 2016 22:56:20:  46000000 
INFO  @ Tue, 17 May 2016 22:56:22:  47000000 
INFO  @ Tue, 17 May 2016 22:56:25:  48000000 
INFO  @ Tue, 17 May 2016 22:56:27:  49000000 
INFO  @ Tue, 17 May 2016 22:56:29:  50000000 
INFO  @ Tue, 17 May 2016 22:56:31:  51000000 
INFO  @ Tue, 17 May 2016 22:56:33:  52000000 
INFO  @ Tue, 17 May 2016 22:56:35:  53000000 
INFO  @ Tue, 17 May 2016 22:56:37:  54000000 
INFO  @ Tue, 17 May 2016 22:56:39:  55000000 
INFO  @ Tue, 17 May 2016 22:56:41:  56000000 
INFO  @ Tue, 17 May 2016 22:56:43:  57000000 
INFO  @ Tue, 17 May 2016 22:56:45:  58000000 
INFO  @ Tue, 17 May 2016 22:56:47:  59000000 
INFO  @ Tue, 17 May 2016 22:56:49:  60000000 
INFO  @ Tue, 17 May 2016 22:56:51:  61000000 
INFO  @ Tue, 17 May 2016 22:56:53:  62000000 
INFO  @ Tue, 17 May 2016 22:56:55:  63000000 
INFO  @ Tue, 17 May 2016 22:56:58:  64000000 
INFO  @ Tue, 17 May 2016 22:57:00:  65000000 
INFO  @ Tue, 17 May 2016 22:57:02:  66000000 
INFO  @ Tue, 17 May 2016 22:57:04:  67000000 
INFO  @ Tue, 17 May 2016 22:57:06:  68000000 
INFO  @ Tue, 17 May 2016 22:57:08:  69000000 
INFO  @ Tue, 17 May 2016 22:57:10:  70000000 
INFO  @ Tue, 17 May 2016 22:57:12:  71000000 
INFO  @ Tue, 17 May 2016 22:57:14:  72000000 
INFO  @ Tue, 17 May 2016 22:57:16:  73000000 
INFO  @ Tue, 17 May 2016 22:57:18:  74000000 
INFO  @ Tue, 17 May 2016 22:57:20:  75000000 
INFO  @ Tue, 17 May 2016 22:57:22:  76000000 
INFO  @ Tue, 17 May 2016 22:57:24:  77000000 
INFO  @ Tue, 17 May 2016 22:57:26:  78000000 
INFO  @ Tue, 17 May 2016 22:57:28:  79000000 
INFO  @ Tue, 17 May 2016 22:57:30:  80000000 
INFO  @ Tue, 17 May 2016 22:57:33:  81000000 
INFO  @ Tue, 17 May 2016 22:57:35:  82000000 
INFO  @ Tue, 17 May 2016 22:57:37:  83000000 
INFO  @ Tue, 17 May 2016 22:57:39:  84000000 
INFO  @ Tue, 17 May 2016 22:57:41:  85000000 
INFO  @ Tue, 17 May 2016 22:57:43:  86000000 
INFO  @ Tue, 17 May 2016 22:57:45:  87000000 
INFO  @ Tue, 17 May 2016 22:57:47:  88000000 
INFO  @ Tue, 17 May 2016 22:57:49:  89000000 
INFO  @ Tue, 17 May 2016 22:57:51:  90000000 
INFO  @ Tue, 17 May 2016 22:57:53:  91000000 
INFO  @ Tue, 17 May 2016 22:57:55:  92000000 
INFO  @ Tue, 17 May 2016 22:57:57:  93000000 
INFO  @ Tue, 17 May 2016 22:57:59:  94000000 
INFO  @ Tue, 17 May 2016 22:58:01:  95000000 
INFO  @ Tue, 17 May 2016 22:58:03:  96000000 
INFO  @ Tue, 17 May 2016 22:58:05:  97000000 
INFO  @ Tue, 17 May 2016 22:58:15: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 22:58:15: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 22:58:15: #1  total tags in treatment: 97386836 
INFO  @ Tue, 17 May 2016 22:58:15: #1 finished! 
INFO  @ Tue, 17 May 2016 22:58:15: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 22:58:15: #2 Skipped... 
INFO  @ Tue, 17 May 2016 22:58:15: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 22:58:15: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 22:58:15: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 22:58:15: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 22:58:15: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 22:58:15: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 23:02:28: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 23:02:28: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 23:02:28: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 23:02:28: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 23:02:28: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 23:15:42: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 23:15:48: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 23:15:52: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 23:15:54: Done!

Num	35
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_40
Name	macs2_atac pooled
Thread	thread_Root
PID	31904

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

Start	2016-05-17 22:40:43
End	2016-05-18 00:18:25
Elapsed	01:37:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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 22:40:45: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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 22:40:45: #1 read tag files... 
INFO  @ Tue, 17 May 2016 22:40:45: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 22:40:47:  1000000 
INFO  @ Tue, 17 May 2016 22:40:49:  2000000 
INFO  @ Tue, 17 May 2016 22:40:51:  3000000 
INFO  @ Tue, 17 May 2016 22:40:53:  4000000 
INFO  @ Tue, 17 May 2016 22:40:55:  5000000 
INFO  @ Tue, 17 May 2016 22:40:57:  6000000 
INFO  @ Tue, 17 May 2016 22:40:59:  7000000 
INFO  @ Tue, 17 May 2016 22:41:01:  8000000 
INFO  @ Tue, 17 May 2016 22:41:03:  9000000 
INFO  @ Tue, 17 May 2016 22:41:05:  10000000 
INFO  @ Tue, 17 May 2016 22:41:06:  11000000 
INFO  @ Tue, 17 May 2016 22:41:08:  12000000 
INFO  @ Tue, 17 May 2016 22:41:10:  13000000 
INFO  @ Tue, 17 May 2016 22:41:12:  14000000 
INFO  @ Tue, 17 May 2016 22:41:14:  15000000 
INFO  @ Tue, 17 May 2016 22:41:16:  16000000 
INFO  @ Tue, 17 May 2016 22:41:18:  17000000 
INFO  @ Tue, 17 May 2016 22:41:20:  18000000 
INFO  @ Tue, 17 May 2016 22:41:22:  19000000 
INFO  @ Tue, 17 May 2016 22:41:24:  20000000 
INFO  @ Tue, 17 May 2016 22:41:26:  21000000 
INFO  @ Tue, 17 May 2016 22:41:28:  22000000 
INFO  @ Tue, 17 May 2016 22:41:30:  23000000 
INFO  @ Tue, 17 May 2016 22:41:32:  24000000 
INFO  @ Tue, 17 May 2016 22:41:34:  25000000 
INFO  @ Tue, 17 May 2016 22:41:36:  26000000 
INFO  @ Tue, 17 May 2016 22:41:38:  27000000 
INFO  @ Tue, 17 May 2016 22:41:40:  28000000 
INFO  @ Tue, 17 May 2016 22:41:42:  29000000 
INFO  @ Tue, 17 May 2016 22:41:44:  30000000 
INFO  @ Tue, 17 May 2016 22:41:46:  31000000 
INFO  @ Tue, 17 May 2016 22:41:48:  32000000 
INFO  @ Tue, 17 May 2016 22:41:50:  33000000 
INFO  @ Tue, 17 May 2016 22:41:52:  34000000 
INFO  @ Tue, 17 May 2016 22:41:54:  35000000 
INFO  @ Tue, 17 May 2016 22:41:56:  36000000 
INFO  @ Tue, 17 May 2016 22:41:57:  37000000 
INFO  @ Tue, 17 May 2016 22:41:59:  38000000 
INFO  @ Tue, 17 May 2016 22:42:01:  39000000 
INFO  @ Tue, 17 May 2016 22:42:04:  40000000 
INFO  @ Tue, 17 May 2016 22:42:06:  41000000 
INFO  @ Tue, 17 May 2016 22:42:07:  42000000 
INFO  @ Tue, 17 May 2016 22:42:09:  43000000 
INFO  @ Tue, 17 May 2016 22:42:11:  44000000 
INFO  @ Tue, 17 May 2016 22:42:13:  45000000 
INFO  @ Tue, 17 May 2016 22:42:15:  46000000 
INFO  @ Tue, 17 May 2016 22:42:17:  47000000 
INFO  @ Tue, 17 May 2016 22:42:19:  48000000 
INFO  @ Tue, 17 May 2016 22:42:21:  49000000 
INFO  @ Tue, 17 May 2016 22:42:23:  50000000 
INFO  @ Tue, 17 May 2016 22:42:25:  51000000 
INFO  @ Tue, 17 May 2016 22:42:27:  52000000 
INFO  @ Tue, 17 May 2016 22:42:29:  53000000 
INFO  @ Tue, 17 May 2016 22:42:30:  54000000 
INFO  @ Tue, 17 May 2016 22:42:33:  55000000 
INFO  @ Tue, 17 May 2016 22:42:35:  56000000 
INFO  @ Tue, 17 May 2016 22:42:37:  57000000 
INFO  @ Tue, 17 May 2016 22:42:39:  58000000 
INFO  @ Tue, 17 May 2016 22:42:41:  59000000 
INFO  @ Tue, 17 May 2016 22:42:43:  60000000 
INFO  @ Tue, 17 May 2016 22:42:45:  61000000 
INFO  @ Tue, 17 May 2016 22:42:47:  62000000 
INFO  @ Tue, 17 May 2016 22:42:49:  63000000 
INFO  @ Tue, 17 May 2016 22:42:50:  64000000 
INFO  @ Tue, 17 May 2016 22:42:52:  65000000 
INFO  @ Tue, 17 May 2016 22:42:54:  66000000 
INFO  @ Tue, 17 May 2016 22:42:56:  67000000 
INFO  @ Tue, 17 May 2016 22:42:58:  68000000 
INFO  @ Tue, 17 May 2016 22:43:00:  69000000 
INFO  @ Tue, 17 May 2016 22:43:02:  70000000 
INFO  @ Tue, 17 May 2016 22:43:04:  71000000 
INFO  @ Tue, 17 May 2016 22:43:06:  72000000 
INFO  @ Tue, 17 May 2016 22:43:07:  73000000 
INFO  @ Tue, 17 May 2016 22:43:09:  74000000 
INFO  @ Tue, 17 May 2016 22:43:11:  75000000 
INFO  @ Tue, 17 May 2016 22:43:13:  76000000 
INFO  @ Tue, 17 May 2016 22:43:15:  77000000 
INFO  @ Tue, 17 May 2016 22:43:17:  78000000 
INFO  @ Tue, 17 May 2016 22:43:19:  79000000 
INFO  @ Tue, 17 May 2016 22:43:21:  80000000 
INFO  @ Tue, 17 May 2016 22:43:23:  81000000 
INFO  @ Tue, 17 May 2016 22:43:24:  82000000 
INFO  @ Tue, 17 May 2016 22:43:26:  83000000 
INFO  @ Tue, 17 May 2016 22:43:28:  84000000 
INFO  @ Tue, 17 May 2016 22:43:31:  85000000 
INFO  @ Tue, 17 May 2016 22:43:33:  86000000 
INFO  @ Tue, 17 May 2016 22:43:37:  87000000 
INFO  @ Tue, 17 May 2016 22:43:39:  88000000 
INFO  @ Tue, 17 May 2016 22:43:41:  89000000 
INFO  @ Tue, 17 May 2016 22:43:43:  90000000 
INFO  @ Tue, 17 May 2016 22:43:45:  91000000 
INFO  @ Tue, 17 May 2016 22:43:49:  92000000 
INFO  @ Tue, 17 May 2016 22:43:51:  93000000 
INFO  @ Tue, 17 May 2016 22:43:53:  94000000 
INFO  @ Tue, 17 May 2016 22:43:55:  95000000 
INFO  @ Tue, 17 May 2016 22:43:57:  96000000 
INFO  @ Tue, 17 May 2016 22:43:59:  97000000 
INFO  @ Tue, 17 May 2016 22:44:08: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 22:44:08: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 22:44:08: #1  total tags in treatment: 97386836 
INFO  @ Tue, 17 May 2016 22:44:08: #1 finished! 
INFO  @ Tue, 17 May 2016 22:44:08: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 22:44:08: #2 Skipped... 
INFO  @ Tue, 17 May 2016 22:44:08: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 22:44:08: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 22:44:08: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 22:44:08: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 22:44:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 22:49:07: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 22:53:33: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 22:53:36: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 22:53:38: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 22:53:40: Done! 
INFO  @ Tue, 17 May 2016 22:53:50: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.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 22:53:50: #1 read tag files... 
INFO  @ Tue, 17 May 2016 22:53:50: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 22:53:52:  1000000 
INFO  @ Tue, 17 May 2016 22:53:54:  2000000 
INFO  @ Tue, 17 May 2016 22:53:56:  3000000 
INFO  @ Tue, 17 May 2016 22:53:58:  4000000 
INFO  @ Tue, 17 May 2016 22:54:00:  5000000 
INFO  @ Tue, 17 May 2016 22:54:02:  6000000 
INFO  @ Tue, 17 May 2016 22:54:04:  7000000 
INFO  @ Tue, 17 May 2016 22:54:06:  8000000 
INFO  @ Tue, 17 May 2016 22:54:08:  9000000 
INFO  @ Tue, 17 May 2016 22:54:10:  10000000 
INFO  @ Tue, 17 May 2016 22:54:12:  11000000 
INFO  @ Tue, 17 May 2016 22:54:14:  12000000 
INFO  @ Tue, 17 May 2016 22:54:16:  13000000 
INFO  @ Tue, 17 May 2016 22:54:18:  14000000 
INFO  @ Tue, 17 May 2016 22:54:20:  15000000 
INFO  @ Tue, 17 May 2016 22:54:22:  16000000 
INFO  @ Tue, 17 May 2016 22:54:24:  17000000 
INFO  @ Tue, 17 May 2016 22:54:26:  18000000 
INFO  @ Tue, 17 May 2016 22:54:28:  19000000 
INFO  @ Tue, 17 May 2016 22:54:30:  20000000 
INFO  @ Tue, 17 May 2016 22:54:33:  21000000 
INFO  @ Tue, 17 May 2016 22:54:35:  22000000 
INFO  @ Tue, 17 May 2016 22:54:37:  23000000 
INFO  @ Tue, 17 May 2016 22:54:39:  24000000 
INFO  @ Tue, 17 May 2016 22:54:41:  25000000 
INFO  @ Tue, 17 May 2016 22:54:43:  26000000 
INFO  @ Tue, 17 May 2016 22:54:45:  27000000 
INFO  @ Tue, 17 May 2016 22:54:47:  28000000 
INFO  @ Tue, 17 May 2016 22:54:49:  29000000 
INFO  @ Tue, 17 May 2016 22:54:51:  30000000 
INFO  @ Tue, 17 May 2016 22:54:53:  31000000 
INFO  @ Tue, 17 May 2016 22:54:55:  32000000 
INFO  @ Tue, 17 May 2016 22:54:57:  33000000 
INFO  @ Tue, 17 May 2016 22:54:59:  34000000 
INFO  @ Tue, 17 May 2016 22:55:01:  35000000 
INFO  @ Tue, 17 May 2016 22:55:03:  36000000 
INFO  @ Tue, 17 May 2016 22:55:05:  37000000 
INFO  @ Tue, 17 May 2016 22:55:07:  38000000 
INFO  @ Tue, 17 May 2016 22:55:09:  39000000 
INFO  @ Tue, 17 May 2016 22:55:11:  40000000 
INFO  @ Tue, 17 May 2016 22:55:13:  41000000 
INFO  @ Tue, 17 May 2016 22:55:15:  42000000 
INFO  @ Tue, 17 May 2016 22:55:17:  43000000 
INFO  @ Tue, 17 May 2016 22:55:19:  44000000 
INFO  @ Tue, 17 May 2016 22:55:21:  45000000 
INFO  @ Tue, 17 May 2016 22:55:23:  46000000 
INFO  @ Tue, 17 May 2016 22:55:25:  47000000 
INFO  @ Tue, 17 May 2016 22:55:27:  48000000 
INFO  @ Tue, 17 May 2016 22:55:29:  49000000 
INFO  @ Tue, 17 May 2016 22:55:31:  50000000 
INFO  @ Tue, 17 May 2016 22:55:33:  51000000 
INFO  @ Tue, 17 May 2016 22:55:35:  52000000 
INFO  @ Tue, 17 May 2016 22:55:37:  53000000 
INFO  @ Tue, 17 May 2016 22:55:39:  54000000 
INFO  @ Tue, 17 May 2016 22:55:41:  55000000 
INFO  @ Tue, 17 May 2016 22:55:43:  56000000 
INFO  @ Tue, 17 May 2016 22:55:45:  57000000 
INFO  @ Tue, 17 May 2016 22:55:47:  58000000 
INFO  @ Tue, 17 May 2016 22:55:49:  59000000 
INFO  @ Tue, 17 May 2016 22:55:51:  60000000 
INFO  @ Tue, 17 May 2016 22:55:53:  61000000 
INFO  @ Tue, 17 May 2016 22:55:55:  62000000 
INFO  @ Tue, 17 May 2016 22:55:57:  63000000 
INFO  @ Tue, 17 May 2016 22:55:59:  64000000 
INFO  @ Tue, 17 May 2016 22:56:01:  65000000 
INFO  @ Tue, 17 May 2016 22:56:03:  66000000 
INFO  @ Tue, 17 May 2016 22:56:05:  67000000 
INFO  @ Tue, 17 May 2016 22:56:07:  68000000 
INFO  @ Tue, 17 May 2016 22:56:09:  69000000 
INFO  @ Tue, 17 May 2016 22:56:11:  70000000 
INFO  @ Tue, 17 May 2016 22:56:13:  71000000 
INFO  @ Tue, 17 May 2016 22:56:15:  72000000 
INFO  @ Tue, 17 May 2016 22:56:17:  73000000 
INFO  @ Tue, 17 May 2016 22:56:19:  74000000 
INFO  @ Tue, 17 May 2016 22:56:21:  75000000 
INFO  @ Tue, 17 May 2016 22:56:23:  76000000 
INFO  @ Tue, 17 May 2016 22:56:25:  77000000 
INFO  @ Tue, 17 May 2016 22:56:27:  78000000 
INFO  @ Tue, 17 May 2016 22:56:29:  79000000 
INFO  @ Tue, 17 May 2016 22:56:31:  80000000 
INFO  @ Tue, 17 May 2016 22:56:33:  81000000 
INFO  @ Tue, 17 May 2016 22:56:35:  82000000 
INFO  @ Tue, 17 May 2016 22:56:37:  83000000 
INFO  @ Tue, 17 May 2016 22:56:39:  84000000 
INFO  @ Tue, 17 May 2016 22:56:41:  85000000 
INFO  @ Tue, 17 May 2016 22:56:43:  86000000 
INFO  @ Tue, 17 May 2016 22:56:45:  87000000 
INFO  @ Tue, 17 May 2016 22:56:47:  88000000 
INFO  @ Tue, 17 May 2016 22:56:49:  89000000 
INFO  @ Tue, 17 May 2016 22:56:51:  90000000 
INFO  @ Tue, 17 May 2016 22:56:53:  91000000 
INFO  @ Tue, 17 May 2016 22:56:55:  92000000 
INFO  @ Tue, 17 May 2016 22:56:57:  93000000 
INFO  @ Tue, 17 May 2016 22:56:59:  94000000 
INFO  @ Tue, 17 May 2016 22:57:01:  95000000 
INFO  @ Tue, 17 May 2016 22:57:03:  96000000 
INFO  @ Tue, 17 May 2016 22:57:05:  97000000 
INFO  @ Tue, 17 May 2016 22:57:14: #1 tag size is determined as 67 bps 
INFO  @ Tue, 17 May 2016 22:57:14: #1 tag size = 67 
INFO  @ Tue, 17 May 2016 22:57:14: #1  total tags in treatment: 97386836 
INFO  @ Tue, 17 May 2016 22:57:14: #1 finished! 
INFO  @ Tue, 17 May 2016 22:57:14: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 22:57:14: #2 Skipped... 
INFO  @ Tue, 17 May 2016 22:57:14: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 22:57:14: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 22:57:14: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 22:57:14: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 22:57:14: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 22:57:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 23:01:27: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 23:01:27: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 23:01:27: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 23:01:27: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 23:01:27: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 23:12:52: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 23:12:56: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 23:12:59: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_summits.bed 
INFO  @ Tue, 17 May 2016 23:13:00: Done! 
INFO  @ Tue, 17 May 2016 23:13:06: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 23:16:13: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 23:17:17: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 23:18:29: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 23:27:05: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 23:32:07: Finished 'FE'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 23:46:16: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 23:48:59: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 23:49:54: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 23:50:53: Values in your input bedGraph files will be multiplied by 97.386836 ... 
INFO  @ Tue, 17 May 2016 23:59:01: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 18 May 2016 00:01:19: Write bedGraph of scores... 
INFO  @ Wed, 18 May 2016 00:06:03: Finished 'ppois'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_ppois.bdg'!

Num	36
ID	task.callpeak_macs2.macs2_atac_ppr1.pval0.1.line_192.id_41
Name	macs2_atac ppr1.pval0.1
Thread	thread_Root
PID	14876

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

Start	2016-05-18 00:18:26
End	2016-05-18 00:40:04
Elapsed	00:21:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Wed, 18 May 2016 00:18:28: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.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-01
# 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  @ Wed, 18 May 2016 00:18:28: #1 read tag files... 
INFO  @ Wed, 18 May 2016 00:18:28: #1 read treatment tags... 
INFO  @ Wed, 18 May 2016 00:18:30:  1000000 
INFO  @ Wed, 18 May 2016 00:18:32:  2000000 
INFO  @ Wed, 18 May 2016 00:18:35:  3000000 
INFO  @ Wed, 18 May 2016 00:18:37:  4000000 
INFO  @ Wed, 18 May 2016 00:18:39:  5000000 
INFO  @ Wed, 18 May 2016 00:18:41:  6000000 
INFO  @ Wed, 18 May 2016 00:18:43:  7000000 
INFO  @ Wed, 18 May 2016 00:18:45:  8000000 
INFO  @ Wed, 18 May 2016 00:18:47:  9000000 
INFO  @ Wed, 18 May 2016 00:18:49:  10000000 
INFO  @ Wed, 18 May 2016 00:18:51:  11000000 
INFO  @ Wed, 18 May 2016 00:18:53:  12000000 
INFO  @ Wed, 18 May 2016 00:18:56:  13000000 
INFO  @ Wed, 18 May 2016 00:18:58:  14000000 
INFO  @ Wed, 18 May 2016 00:19:00:  15000000 
INFO  @ Wed, 18 May 2016 00:19:02:  16000000 
INFO  @ Wed, 18 May 2016 00:19:04:  17000000 
INFO  @ Wed, 18 May 2016 00:19:06:  18000000 
INFO  @ Wed, 18 May 2016 00:19:08:  19000000 
INFO  @ Wed, 18 May 2016 00:19:10:  20000000 
INFO  @ Wed, 18 May 2016 00:19:12:  21000000 
INFO  @ Wed, 18 May 2016 00:19:15:  22000000 
INFO  @ Wed, 18 May 2016 00:19:17:  23000000 
INFO  @ Wed, 18 May 2016 00:19:19:  24000000 
INFO  @ Wed, 18 May 2016 00:19:21:  25000000 
INFO  @ Wed, 18 May 2016 00:19:23:  26000000 
INFO  @ Wed, 18 May 2016 00:19:25:  27000000 
INFO  @ Wed, 18 May 2016 00:19:27:  28000000 
INFO  @ Wed, 18 May 2016 00:19:29:  29000000 
INFO  @ Wed, 18 May 2016 00:19:31:  30000000 
INFO  @ Wed, 18 May 2016 00:19:33:  31000000 
INFO  @ Wed, 18 May 2016 00:19:35:  32000000 
INFO  @ Wed, 18 May 2016 00:19:37:  33000000 
INFO  @ Wed, 18 May 2016 00:19:40:  34000000 
INFO  @ Wed, 18 May 2016 00:19:42:  35000000 
INFO  @ Wed, 18 May 2016 00:19:44:  36000000 
INFO  @ Wed, 18 May 2016 00:19:46:  37000000 
INFO  @ Wed, 18 May 2016 00:19:48:  38000000 
INFO  @ Wed, 18 May 2016 00:19:50:  39000000 
INFO  @ Wed, 18 May 2016 00:19:52:  40000000 
INFO  @ Wed, 18 May 2016 00:19:54:  41000000 
INFO  @ Wed, 18 May 2016 00:19:56:  42000000 
INFO  @ Wed, 18 May 2016 00:19:58:  43000000 
INFO  @ Wed, 18 May 2016 00:20:00:  44000000 
INFO  @ Wed, 18 May 2016 00:20:02:  45000000 
INFO  @ Wed, 18 May 2016 00:20:04:  46000000 
INFO  @ Wed, 18 May 2016 00:20:06:  47000000 
INFO  @ Wed, 18 May 2016 00:20:08:  48000000 
INFO  @ Wed, 18 May 2016 00:20:11:  49000000 
INFO  @ Wed, 18 May 2016 00:20:13:  50000000 
INFO  @ Wed, 18 May 2016 00:20:15:  51000000 
INFO  @ Wed, 18 May 2016 00:20:17:  52000000 
INFO  @ Wed, 18 May 2016 00:20:19:  53000000 
INFO  @ Wed, 18 May 2016 00:20:21:  54000000 
INFO  @ Wed, 18 May 2016 00:20:27: #1 tag size is determined as 70 bps 
INFO  @ Wed, 18 May 2016 00:20:27: #1 tag size = 70 
INFO  @ Wed, 18 May 2016 00:20:27: #1  total tags in treatment: 54544982 
INFO  @ Wed, 18 May 2016 00:20:27: #1 finished! 
INFO  @ Wed, 18 May 2016 00:20:27: #2 Build Peak Model... 
INFO  @ Wed, 18 May 2016 00:20:27: #2 Skipped... 
INFO  @ Wed, 18 May 2016 00:20:27: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 18 May 2016 00:20:27: #2 Use 150 as fragment length 
INFO  @ Wed, 18 May 2016 00:20:27: #3 Call peaks... 
INFO  @ Wed, 18 May 2016 00:20:27: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Wed, 18 May 2016 00:20:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 18 May 2016 00:23:19: #3 Call peaks for each chromosome... 
INFO  @ Wed, 18 May 2016 00:26:09: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Wed, 18 May 2016 00:26:12: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Wed, 18 May 2016 00:26:14: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Wed, 18 May 2016 00:26:16: Done! 
INFO  @ Wed, 18 May 2016 00:26:25: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 18 May 2016 00:26:25: #1 read tag files... 
INFO  @ Wed, 18 May 2016 00:26:25: #1 read treatment tags... 
INFO  @ Wed, 18 May 2016 00:26:27:  1000000 
INFO  @ Wed, 18 May 2016 00:26:29:  2000000 
INFO  @ Wed, 18 May 2016 00:26:31:  3000000 
INFO  @ Wed, 18 May 2016 00:26:33:  4000000 
INFO  @ Wed, 18 May 2016 00:26:36:  5000000 
INFO  @ Wed, 18 May 2016 00:26:38:  6000000 
INFO  @ Wed, 18 May 2016 00:26:40:  7000000 
INFO  @ Wed, 18 May 2016 00:26:42:  8000000 
INFO  @ Wed, 18 May 2016 00:26:44:  9000000 
INFO  @ Wed, 18 May 2016 00:26:46:  10000000 
INFO  @ Wed, 18 May 2016 00:26:48:  11000000 
INFO  @ Wed, 18 May 2016 00:26:50:  12000000 
INFO  @ Wed, 18 May 2016 00:26:52:  13000000 
INFO  @ Wed, 18 May 2016 00:26:54:  14000000 
INFO  @ Wed, 18 May 2016 00:26:56:  15000000 
INFO  @ Wed, 18 May 2016 00:26:58:  16000000 
INFO  @ Wed, 18 May 2016 00:27:00:  17000000 
INFO  @ Wed, 18 May 2016 00:27:02:  18000000 
INFO  @ Wed, 18 May 2016 00:27:04:  19000000 
INFO  @ Wed, 18 May 2016 00:27:06:  20000000 
INFO  @ Wed, 18 May 2016 00:27:08:  21000000 
INFO  @ Wed, 18 May 2016 00:27:10:  22000000 
INFO  @ Wed, 18 May 2016 00:27:13:  23000000 
INFO  @ Wed, 18 May 2016 00:27:15:  24000000 
INFO  @ Wed, 18 May 2016 00:27:17:  25000000 
INFO  @ Wed, 18 May 2016 00:27:19:  26000000 
INFO  @ Wed, 18 May 2016 00:27:21:  27000000 
INFO  @ Wed, 18 May 2016 00:27:23:  28000000 
INFO  @ Wed, 18 May 2016 00:27:25:  29000000 
INFO  @ Wed, 18 May 2016 00:27:27:  30000000 
INFO  @ Wed, 18 May 2016 00:27:29:  31000000 
INFO  @ Wed, 18 May 2016 00:27:31:  32000000 
INFO  @ Wed, 18 May 2016 00:27:33:  33000000 
INFO  @ Wed, 18 May 2016 00:27:35:  34000000 
INFO  @ Wed, 18 May 2016 00:27:37:  35000000 
INFO  @ Wed, 18 May 2016 00:27:39:  36000000 
INFO  @ Wed, 18 May 2016 00:27:41:  37000000 
INFO  @ Wed, 18 May 2016 00:27:43:  38000000 
INFO  @ Wed, 18 May 2016 00:27:45:  39000000 
INFO  @ Wed, 18 May 2016 00:27:47:  40000000 
INFO  @ Wed, 18 May 2016 00:27:49:  41000000 
INFO  @ Wed, 18 May 2016 00:27:51:  42000000 
INFO  @ Wed, 18 May 2016 00:27:53:  43000000 
INFO  @ Wed, 18 May 2016 00:27:55:  44000000 
INFO  @ Wed, 18 May 2016 00:27:57:  45000000 
INFO  @ Wed, 18 May 2016 00:27:59:  46000000 
INFO  @ Wed, 18 May 2016 00:28:01:  47000000 
INFO  @ Wed, 18 May 2016 00:28:03:  48000000 
INFO  @ Wed, 18 May 2016 00:28:05:  49000000 
INFO  @ Wed, 18 May 2016 00:28:07:  50000000 
INFO  @ Wed, 18 May 2016 00:28:09:  51000000 
INFO  @ Wed, 18 May 2016 00:28:11:  52000000 
INFO  @ Wed, 18 May 2016 00:28:13:  53000000 
INFO  @ Wed, 18 May 2016 00:28:15:  54000000 
INFO  @ Wed, 18 May 2016 00:28:21: #1 tag size is determined as 70 bps 
INFO  @ Wed, 18 May 2016 00:28:21: #1 tag size = 70 
INFO  @ Wed, 18 May 2016 00:28:21: #1  total tags in treatment: 54544982 
INFO  @ Wed, 18 May 2016 00:28:21: #1 finished! 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Build Peak Model... 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Skipped... 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Use 150 as fragment length 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Call peaks... 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Going to call summits inside each peak ... 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 18 May 2016 00:31:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 18 May 2016 00:31:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Wed, 18 May 2016 00:31:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Wed, 18 May 2016 00:31:14: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 18 May 2016 00:31:14: #3 Call peaks for each chromosome... 
INFO  @ Wed, 18 May 2016 00:39:48: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Wed, 18 May 2016 00:39:53: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Wed, 18 May 2016 00:39:57: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Wed, 18 May 2016 00:39:59: Done!

Num	37
ID	task.callpeak_macs2.macs2_atac_ppr2.pval0.1.line_192.id_42
Name	macs2_atac ppr2.pval0.1
Thread	thread_Root
PID	14878

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

Start	2016-05-18 00:18:26
End	2016-05-18 00:39:59
Elapsed	00:21:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.gappedPeak.gz
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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.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/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes" "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/signal/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Wed, 18 May 2016 00:18:28: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.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-01
# 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  @ Wed, 18 May 2016 00:18:28: #1 read tag files... 
INFO  @ Wed, 18 May 2016 00:18:28: #1 read treatment tags... 
INFO  @ Wed, 18 May 2016 00:18:30:  1000000 
INFO  @ Wed, 18 May 2016 00:18:32:  2000000 
INFO  @ Wed, 18 May 2016 00:18:34:  3000000 
INFO  @ Wed, 18 May 2016 00:18:36:  4000000 
INFO  @ Wed, 18 May 2016 00:18:38:  5000000 
INFO  @ Wed, 18 May 2016 00:18:40:  6000000 
INFO  @ Wed, 18 May 2016 00:18:43:  7000000 
INFO  @ Wed, 18 May 2016 00:18:45:  8000000 
INFO  @ Wed, 18 May 2016 00:18:47:  9000000 
INFO  @ Wed, 18 May 2016 00:18:49:  10000000 
INFO  @ Wed, 18 May 2016 00:18:51:  11000000 
INFO  @ Wed, 18 May 2016 00:18:53:  12000000 
INFO  @ Wed, 18 May 2016 00:18:55:  13000000 
INFO  @ Wed, 18 May 2016 00:18:57:  14000000 
INFO  @ Wed, 18 May 2016 00:18:59:  15000000 
INFO  @ Wed, 18 May 2016 00:19:01:  16000000 
INFO  @ Wed, 18 May 2016 00:19:03:  17000000 
INFO  @ Wed, 18 May 2016 00:19:05:  18000000 
INFO  @ Wed, 18 May 2016 00:19:07:  19000000 
INFO  @ Wed, 18 May 2016 00:19:09:  20000000 
INFO  @ Wed, 18 May 2016 00:19:11:  21000000 
INFO  @ Wed, 18 May 2016 00:19:13:  22000000 
INFO  @ Wed, 18 May 2016 00:19:15:  23000000 
INFO  @ Wed, 18 May 2016 00:19:17:  24000000 
INFO  @ Wed, 18 May 2016 00:19:19:  25000000 
INFO  @ Wed, 18 May 2016 00:19:21:  26000000 
INFO  @ Wed, 18 May 2016 00:19:23:  27000000 
INFO  @ Wed, 18 May 2016 00:19:25:  28000000 
INFO  @ Wed, 18 May 2016 00:19:27:  29000000 
INFO  @ Wed, 18 May 2016 00:19:29:  30000000 
INFO  @ Wed, 18 May 2016 00:19:31:  31000000 
INFO  @ Wed, 18 May 2016 00:19:33:  32000000 
INFO  @ Wed, 18 May 2016 00:19:35:  33000000 
INFO  @ Wed, 18 May 2016 00:19:37:  34000000 
INFO  @ Wed, 18 May 2016 00:19:39:  35000000 
INFO  @ Wed, 18 May 2016 00:19:41:  36000000 
INFO  @ Wed, 18 May 2016 00:19:43:  37000000 
INFO  @ Wed, 18 May 2016 00:19:45:  38000000 
INFO  @ Wed, 18 May 2016 00:19:47:  39000000 
INFO  @ Wed, 18 May 2016 00:19:49:  40000000 
INFO  @ Wed, 18 May 2016 00:19:51:  41000000 
INFO  @ Wed, 18 May 2016 00:19:53:  42000000 
INFO  @ Wed, 18 May 2016 00:19:55:  43000000 
INFO  @ Wed, 18 May 2016 00:19:57:  44000000 
INFO  @ Wed, 18 May 2016 00:19:59:  45000000 
INFO  @ Wed, 18 May 2016 00:20:01:  46000000 
INFO  @ Wed, 18 May 2016 00:20:03:  47000000 
INFO  @ Wed, 18 May 2016 00:20:05:  48000000 
INFO  @ Wed, 18 May 2016 00:20:08:  49000000 
INFO  @ Wed, 18 May 2016 00:20:10:  50000000 
INFO  @ Wed, 18 May 2016 00:20:12:  51000000 
INFO  @ Wed, 18 May 2016 00:20:14:  52000000 
INFO  @ Wed, 18 May 2016 00:20:16:  53000000 
INFO  @ Wed, 18 May 2016 00:20:18:  54000000 
INFO  @ Wed, 18 May 2016 00:20:23: #1 tag size is determined as 55 bps 
INFO  @ Wed, 18 May 2016 00:20:23: #1 tag size = 55 
INFO  @ Wed, 18 May 2016 00:20:23: #1  total tags in treatment: 54544980 
INFO  @ Wed, 18 May 2016 00:20:23: #1 finished! 
INFO  @ Wed, 18 May 2016 00:20:23: #2 Build Peak Model... 
INFO  @ Wed, 18 May 2016 00:20:23: #2 Skipped... 
INFO  @ Wed, 18 May 2016 00:20:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 18 May 2016 00:20:23: #2 Use 150 as fragment length 
INFO  @ Wed, 18 May 2016 00:20:23: #3 Call peaks... 
INFO  @ Wed, 18 May 2016 00:20:23: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Wed, 18 May 2016 00:20:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 18 May 2016 00:23:17: #3 Call peaks for each chromosome... 
INFO  @ Wed, 18 May 2016 00:26:08: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Wed, 18 May 2016 00:26:11: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Wed, 18 May 2016 00:26:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Wed, 18 May 2016 00:26:15: Done! 
INFO  @ Wed, 18 May 2016 00:26:24: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 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 off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 18 May 2016 00:26:24: #1 read tag files... 
INFO  @ Wed, 18 May 2016 00:26:24: #1 read treatment tags... 
INFO  @ Wed, 18 May 2016 00:26:26:  1000000 
INFO  @ Wed, 18 May 2016 00:26:28:  2000000 
INFO  @ Wed, 18 May 2016 00:26:30:  3000000 
INFO  @ Wed, 18 May 2016 00:26:32:  4000000 
INFO  @ Wed, 18 May 2016 00:26:34:  5000000 
INFO  @ Wed, 18 May 2016 00:26:36:  6000000 
INFO  @ Wed, 18 May 2016 00:26:38:  7000000 
INFO  @ Wed, 18 May 2016 00:26:41:  8000000 
INFO  @ Wed, 18 May 2016 00:26:43:  9000000 
INFO  @ Wed, 18 May 2016 00:26:45:  10000000 
INFO  @ Wed, 18 May 2016 00:26:47:  11000000 
INFO  @ Wed, 18 May 2016 00:26:49:  12000000 
INFO  @ Wed, 18 May 2016 00:26:51:  13000000 
INFO  @ Wed, 18 May 2016 00:26:53:  14000000 
INFO  @ Wed, 18 May 2016 00:26:55:  15000000 
INFO  @ Wed, 18 May 2016 00:26:57:  16000000 
INFO  @ Wed, 18 May 2016 00:26:59:  17000000 
INFO  @ Wed, 18 May 2016 00:27:01:  18000000 
INFO  @ Wed, 18 May 2016 00:27:03:  19000000 
INFO  @ Wed, 18 May 2016 00:27:06:  20000000 
INFO  @ Wed, 18 May 2016 00:27:08:  21000000 
INFO  @ Wed, 18 May 2016 00:27:10:  22000000 
INFO  @ Wed, 18 May 2016 00:27:12:  23000000 
INFO  @ Wed, 18 May 2016 00:27:14:  24000000 
INFO  @ Wed, 18 May 2016 00:27:16:  25000000 
INFO  @ Wed, 18 May 2016 00:27:18:  26000000 
INFO  @ Wed, 18 May 2016 00:27:20:  27000000 
INFO  @ Wed, 18 May 2016 00:27:22:  28000000 
INFO  @ Wed, 18 May 2016 00:27:24:  29000000 
INFO  @ Wed, 18 May 2016 00:27:26:  30000000 
INFO  @ Wed, 18 May 2016 00:27:28:  31000000 
INFO  @ Wed, 18 May 2016 00:27:30:  32000000 
INFO  @ Wed, 18 May 2016 00:27:32:  33000000 
INFO  @ Wed, 18 May 2016 00:27:34:  34000000 
INFO  @ Wed, 18 May 2016 00:27:36:  35000000 
INFO  @ Wed, 18 May 2016 00:27:39:  36000000 
INFO  @ Wed, 18 May 2016 00:27:41:  37000000 
INFO  @ Wed, 18 May 2016 00:27:43:  38000000 
INFO  @ Wed, 18 May 2016 00:27:45:  39000000 
INFO  @ Wed, 18 May 2016 00:27:47:  40000000 
INFO  @ Wed, 18 May 2016 00:27:49:  41000000 
INFO  @ Wed, 18 May 2016 00:27:51:  42000000 
INFO  @ Wed, 18 May 2016 00:27:53:  43000000 
INFO  @ Wed, 18 May 2016 00:27:55:  44000000 
INFO  @ Wed, 18 May 2016 00:27:57:  45000000 
INFO  @ Wed, 18 May 2016 00:27:59:  46000000 
INFO  @ Wed, 18 May 2016 00:28:01:  47000000 
INFO  @ Wed, 18 May 2016 00:28:03:  48000000 
INFO  @ Wed, 18 May 2016 00:28:05:  49000000 
INFO  @ Wed, 18 May 2016 00:28:07:  50000000 
INFO  @ Wed, 18 May 2016 00:28:09:  51000000 
INFO  @ Wed, 18 May 2016 00:28:11:  52000000 
INFO  @ Wed, 18 May 2016 00:28:13:  53000000 
INFO  @ Wed, 18 May 2016 00:28:15:  54000000 
INFO  @ Wed, 18 May 2016 00:28:21: #1 tag size is determined as 55 bps 
INFO  @ Wed, 18 May 2016 00:28:21: #1 tag size = 55 
INFO  @ Wed, 18 May 2016 00:28:21: #1  total tags in treatment: 54544980 
INFO  @ Wed, 18 May 2016 00:28:21: #1 finished! 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Build Peak Model... 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Skipped... 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 18 May 2016 00:28:21: #2 Use 150 as fragment length 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Call peaks... 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Going to call summits inside each peak ... 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Wed, 18 May 2016 00:28:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 18 May 2016 00:31:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 18 May 2016 00:31:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Wed, 18 May 2016 00:31:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Wed, 18 May 2016 00:31:14: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 18 May 2016 00:31:14: #3 Call peaks for each chromosome... 
INFO  @ Wed, 18 May 2016 00:39:43: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Wed, 18 May 2016 00:39:49: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Wed, 18 May 2016 00:39:52: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Wed, 18 May 2016 00:39:54: Done!

Num	38
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_43
Name	filt_top_peaks rep1
Thread	thread_Root
PID	25505

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:14
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	39
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_44
Name	filt_top_peaks rep1
Thread	thread_Root
PID	25510

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:13
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	40
ID	task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_45
Name	filt_top_peaks rep1-pr1
Thread	thread_Root
PID	25518

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:14
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	41
ID	task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_46
Name	filt_top_peaks rep1-pr2
Thread	thread_Root
PID	25532

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:14
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	42
ID	task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_47
Name	filt_top_peaks rep1-pr1
Thread	thread_Root
PID	25546

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:13
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	43
ID	task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_48
Name	filt_top_peaks rep1-pr2
Thread	thread_Root
PID	25560

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:13
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	44
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_49
Name	filt_top_peaks rep2
Thread	thread_Root
PID	25575

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:11
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	45
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_50
Name	filt_top_peaks rep2
Thread	thread_Root
PID	25594

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:10
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	46
ID	task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_51
Name	filt_top_peaks rep2-pr1
Thread	thread_Root
PID	25612

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:12
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	47
ID	task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_52
Name	filt_top_peaks rep2-pr2
Thread	thread_Root
PID	25628

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:11
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	48
ID	task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_53
Name	filt_top_peaks rep2-pr1
Thread	thread_Root
PID	25645

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:12
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	49
ID	task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_54
Name	filt_top_peaks rep2-pr2
Thread	thread_Root
PID	25662

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:12
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	50
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_55
Name	filt_top_peaks pooled
Thread	thread_Root
PID	25679

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:13
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	51
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_56
Name	filt_top_peaks pooled
Thread	thread_Root
PID	25700

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:11
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	52
ID	task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_57
Name	filt_top_peaks ppr1
Thread	thread_Root
PID	25714

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:12
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	53
ID	task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_58
Name	filt_top_peaks ppr2
Thread	thread_Root
PID	25727

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

Start	2016-05-18 00:40:04
End	2016-05-18 00:40:12
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	54
ID	task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_59
Name	filt_top_peaks ppr1
Thread	thread_Root
PID	25750

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

Start	2016-05-18 00:40:05
End	2016-05-18 00:40:12
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	55
ID	task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_60
Name	filt_top_peaks ppr2
Thread	thread_Root
PID	25777

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

Start	2016-05-18 00:40:05
End	2016-05-18 00:40:12
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	56
ID	task.callpeak_etc.naive_overlap_thresh_peak.line_125.id_61
Name	naive_overlap_thresh peak
Thread	thread_Root
PID	27021

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

Start	2016-05-18 00:40:15
End	2016-05-18 00:40:16
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz
Dependencies

 
# SYS command. line 127

 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 130

 intersectBed -wo -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz -b /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz | awk 'BEGIN{FS="	";OFS="	"} {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 /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz

# SYS command. line 133

 intersectBed -wo -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz -b /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.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 /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.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 -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 138

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz

# SYS command. line 140

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInPsRep1AndPsRep2.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz has inconsistent naming convention for record:
mm9_chr1	24618413	24622890	Peak_3	44072	.	2.72091	4407.24023	4399.80811	1854
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz has inconsistent naming convention for record:
chr1	565542	565907	Peak_3	64994	.	4.99122	6499.44434	6491.96240	186
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz has inconsistent naming convention for record:
mm9_chr2	69193524	69193792	Peak_3	54424	.	64.46676	5442.41309	5434.64111	131
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz has inconsistent naming convention for record:
mm9_chr2	69193524	69193792	Peak_2	54995	.	64.53560	5499.52100	5491.60107	131

Num	57
ID	task.callpeak_etc.naive_overlap_thresh_gpeak.line_125.id_62
Name	naive_overlap_thresh gpeak
Thread	thread_Root
PID	27027

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

Start	2016-05-18 00:40:15
End	2016-05-18 00:40:16
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.gz
Dependencies

 
# SYS command. line 127

 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 130

 intersectBed -wo -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz -b /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz | awk 'BEGIN{FS="	";OFS="	"} {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 /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz

# SYS command. line 133

 intersectBed -wo -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz -b /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.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 /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.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 -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 138

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.gz

# SYS command. line 140

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInPsRep1AndPsRep2.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz has inconsistent naming convention for record:
mm9_chr1	197174932	197175106	Peak_425645	2	.	197174932	197175106	0	1	174	0	1.04309	0.92201	0.22296
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz has inconsistent naming convention for record:
mm9_chr1	197163006	197163912	Peak_339296	3	.	197163006	197163912	0	2	1,1	0,905	1.01354	0.95861	0.35885
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz has inconsistent naming convention for record:
mm9_chr1	197163052	197163511	Peak_341494	1	.	197163052	197163511	0	2	1,1	0,458	1.14747	1.19021	0.16961
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz has inconsistent naming convention for record:
mm9_chr1	197118193	197118343	Peak_290613	7	.	197118193	197118343	0	2	1,1	0,149	1.14491	1.73336	0.77482

Num	58
ID	task.idr.idr2_rep1_rep2.line_72.id_63
Name	idr2 rep1-rep2
Thread	thread_Root
PID	27035

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

Start	2016-05-18 00:40:15
End	2016-05-18 00:40:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 74

 if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 76

 idr --samples /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 80

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 83

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.12-col.bed.gz

# SYS command. line 89

 bedtools intersect -v -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz

# SYS command. line 90

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz

# SYS command. line 93

 gzip -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]

Num	59
ID	task.idr.idr2_rep1_pr.line_72.id_64
Name	idr2 rep1-pr
Thread	thread_Root
PID	27047

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

Start	2016-05-18 00:40:15
End	2016-05-18 00:40:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 74

 if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 76

 idr --samples /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 80

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 83

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.12-col.bed.gz

# SYS command. line 89

 bedtools intersect -v -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 90

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.12-col.bed.gz

# SYS command. line 93

 gzip -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.13-col.bed.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]

Num	60
ID	task.idr.idr2_rep2_pr.line_72.id_65
Name	idr2 rep2-pr
Thread	thread_Root
PID	27057

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

Start	2016-05-18 00:40:15
End	2016-05-18 00:40:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 74

 if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 76

 idr --samples /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 80

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 83

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.12-col.bed.gz

# SYS command. line 89

 bedtools intersect -v -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 90

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.12-col.bed.gz

# SYS command. line 93

 gzip -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.13-col.bed.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]

Num	61
ID	task.idr.idr2_ppr.line_72.id_66
Name	idr2 ppr
Thread	thread_Root
PID	27073

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

Start	2016-05-18 00:40:15
End	2016-05-18 00:40:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 74

 if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 76

 idr --samples /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 80

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 83

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.12-col.bed.gz

# SYS command. line 89

 bedtools intersect -v -a /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 90

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.12-col.bed.gz

# SYS command. line 93

 gzip -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.13-col.bed.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]

Type	Name	Value
string{}	filt_gpeak	{2=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz, 1=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz}
string	filt_gpeak_pooled	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
string	filt_gpeak_ppr1	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
string	filt_gpeak_ppr2	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
string{}	filt_gpeak_pr1	{2=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz, 1=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz}
string{}	filt_gpeak_pr2	{2=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz, 1=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz}
string{}	filt_peak	{2=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz, 1=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz}
string	filt_peak_pooled	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
string	filt_peak_ppr1	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
string	filt_peak_ppr2	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
string{}	filt_peak_pr1	{2=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz, 1=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz}
string{}	filt_peak_pr2	{2=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz, 1=/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz}
string	idr_o_dir	/srv/scratch/annashch/output/4x_experiments/baseChroms_multiMap_3hr/peak/idr

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope