Script file	/srv/scratch/annashch/bds_atac/atac.bds
Program ID	atac.bds.20160519_090716_112
Start time	2016-05-19 09:07:16
Run time	12:35:29.102
Tasks executed	68
Tasks failed	2
Tasks failed names	ataqc rep1 ataqc rep2
Arguments*	[-out_dir, 4x_experiments/baseChroms_noMultiMap_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, -par_lvl, 5, -nth_bwt2, 6]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160519_090716_112/task.postalign_bed.pool_tag_reps.line_405.id_36 atac.bds.20160519_090716_112/task.postalign_bed.pool_tag_reps_pr1.line_405.id_37 atac.bds.20160519_090716_112/task.postalign_bed.pool_tag_reps_pr2.line_405.id_38 atac.bds.20160519_090716_112/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_39 atac.bds.20160519_090716_112/task.callpeak_macs2.macs2_atac_pooled.line_192.id_40 atac.bds.20160519_090716_112/task.callpeak_macs2.macs2_atac_ppr1.pval0.1.line_192.id_41 atac.bds.20160519_090716_112/task.callpeak_macs2.macs2_atac_ppr2.pval0.1.line_192.id_42 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_43 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_44 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_45 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_46 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_47 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_48 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_49 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_50 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_51 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_52 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_53 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_54 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_55 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_56 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_57 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_58 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_59 atac.bds.20160519_090716_112/task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_60 atac.bds.20160519_090716_112/task.callpeak_etc.naive_overlap_thresh_peak.line_125.id_61 atac.bds.20160519_090716_112/task.callpeak_etc.naive_overlap_thresh_gpeak.line_125.id_62 atac.bds.20160519_090716_112/task.idr.idr2_rep1_rep2.line_72.id_63 atac.bds.20160519_090716_112/task.idr.idr2_rep1_pr.line_72.id_64 atac.bds.20160519_090716_112/task.idr.idr2_rep2_pr.line_72.id_65 atac.bds.20160519_090716_112/task.idr.idr2_ppr.line_72.id_66 atac.bds.20160519_090716_112/task.base.line_414.id_75 atac.bds.20160519_090716_112/task.base.line_414.id_76 atac.bds.20160519_090716_112/task.base.line_414.id_77 atac.bds.20160519_090716_112/task.base.line_414.id_78 atac.bds.20160519_090716_112/task.idr.idr_final_qc.line_210.id_79
thread_21	thread_Root	atac.bds.20160519_090716_112_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_131.id_7 atac.bds.20160519_090716_112_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9 atac.bds.20160519_090716_112_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_23 atac.bds.20160519_090716_112_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_24 atac.bds.20160519_090716_112_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_25 atac.bds.20160519_090716_112_parallel_21/task.postalign_bed.spr_PE_rep2.line_248.id_26 atac.bds.20160519_090716_112_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_27 atac.bds.20160519_090716_112_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_28 atac.bds.20160519_090716_112_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_29 atac.bds.20160519_090716_112_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_30 atac.bds.20160519_090716_112_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_31 atac.bds.20160519_090716_112_parallel_21/task.callpeak_macs2.macs2_atac_rep2_pr1.pval0.1.line_192.id_32 atac.bds.20160519_090716_112_parallel_21/task.callpeak_macs2.macs2_atac_rep2_pr2.pval0.1.line_192.id_33 atac.bds.20160519_090716_112_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_34 atac.bds.20160519_090716_112_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_35
thread_20	thread_Root	atac.bds.20160519_090716_112_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_131.id_6 atac.bds.20160519_090716_112_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160519_090716_112_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_10 atac.bds.20160519_090716_112_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_11 atac.bds.20160519_090716_112_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12 atac.bds.20160519_090716_112_parallel_20/task.postalign_bed.spr_PE_rep1.line_248.id_13 atac.bds.20160519_090716_112_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_14 atac.bds.20160519_090716_112_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_15 atac.bds.20160519_090716_112_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_16 atac.bds.20160519_090716_112_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_17 atac.bds.20160519_090716_112_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_18 atac.bds.20160519_090716_112_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr1.pval0.1.line_192.id_19 atac.bds.20160519_090716_112_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr2.pval0.1.line_192.id_20 atac.bds.20160519_090716_112_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_21 atac.bds.20160519_090716_112_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_22
thread_143	thread_Root	atac.bds.20160519_090716_112_parallel_143/task.atac.ataqc_rep2.line_861.id_81
thread_142	thread_Root	atac.bds.20160519_090716_112_parallel_142/task.atac.ataqc_rep1.line_861.id_80

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	19350

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	6
Mem

Start	2016-05-19 09:07:17
End	2016-05-19 12:11:35
Elapsed	03:04:17
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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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  -X2000 --mm --threads 6 -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_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 6 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 6 -o /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	19355

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	6
Mem

Start	2016-05-19 09:07:17
End	2016-05-19 13:36:42
Elapsed	04:29:25
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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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  -X2000 --mm --threads 6 -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_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 6 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 6 -o /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	33076

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

Start	2016-05-19 12:11:36
End	2016-05-19 15:08:11
Elapsed	02:56:34
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.PE2SE.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

 samtools fixmate -r /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam

   
--------------------Stdout--------------------



 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 34 files...
[bam_sort_core] merging from 34 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu May 19 13:43:13 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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
[Thu May 19 13:43:13 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	2016-05-19 13:43:13	MarkDuplicates	Start of doWork freeMemory: 254891160; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-19 13:43:13	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-19 13:43:13	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-19 13:43:19	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:127,974,272
INFO	2016-05-19 13:43:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:43:24	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr11:120,797,444
INFO	2016-05-19 13:43:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:43:29	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    5s.  Last read position: chr12:104,848,521
INFO	2016-05-19 13:43:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:43:34	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    5s.  Last read position: chr14:45,607,445
INFO	2016-05-19 13:43:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:43:42	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    7s.  Last read position: chr15:79,627,458
INFO	2016-05-19 13:43:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:43:48	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    6s.  Last read position: chr17:33,337,267
INFO	2016-05-19 13:43:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:43:53	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    5s.  Last read position: chr19:8,372,946
INFO	2016-05-19 13:43:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:44:00	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    6s.  Last read position: chr1:57,463,660
INFO	2016-05-19 13:44:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:44:04	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    4s.  Last read position: chr1:201,482,104
INFO	2016-05-19 13:44:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 13:44:09	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    4s.  Last read position: chr21:29,808,992
INFO	2016-05-19 13:44:09	MarkDuplicates	Tracking 52 as yet unmatched pairs. 52 records in RAM.
INFO	2016-05-19 13:44:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    5s.  Last read position: chr2:66,614,488
INFO	2016-05-19 13:44:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:44:22	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    7s.  Last read position: chr2:208,910,954
INFO	2016-05-19 13:44:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:44:26	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    4s.  Last read position: chr3:89,439,052
INFO	2016-05-19 13:44:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:44:33	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    6s.  Last read position: chr4:15,665,938
INFO	2016-05-19 13:44:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:44:51	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:   17s.  Last read position: chr4:182,868,549
INFO	2016-05-19 13:44:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:44:55	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    4s.  Last read position: chr5:135,351,420
INFO	2016-05-19 13:44:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:45:00	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    5s.  Last read position: chr6:56,823,975
INFO	2016-05-19 13:45:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:45:06	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    5s.  Last read position: chr7:32,588,075
INFO	2016-05-19 13:45:06	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 13:45:11	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    5s.  Last read position: chr8:22,508,522
INFO	2016-05-19 13:45:11	MarkDuplicates	Tracking 30 as yet unmatched pairs. 30 records in RAM.
INFO	2016-05-19 13:45:18	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    6s.  Last read position: chr9:15,552,445
INFO	2016-05-19 13:45:18	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-19 13:45:22	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    4s.  Last read position: chrM:401
INFO	2016-05-19 13:45:22	MarkDuplicates	Tracking 26734 as yet unmatched pairs. 26734 records in RAM.
INFO	2016-05-19 13:45:26	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,366
INFO	2016-05-19 13:45:26	MarkDuplicates	Tracking 5830 as yet unmatched pairs. 5830 records in RAM.
INFO	2016-05-19 13:45:30	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,396
INFO	2016-05-19 13:45:30	MarkDuplicates	Tracking 28674 as yet unmatched pairs. 28674 records in RAM.
INFO	2016-05-19 13:45:34	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,360
INFO	2016-05-19 13:45:34	MarkDuplicates	Tracking 19828 as yet unmatched pairs. 19828 records in RAM.
INFO	2016-05-19 13:45:41	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    6s.  Last read position: chrM:7,668
INFO	2016-05-19 13:45:41	MarkDuplicates	Tracking 14088 as yet unmatched pairs. 14088 records in RAM.
INFO	2016-05-19 13:45:45	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    4s.  Last read position: chrM:9,872
INFO	2016-05-19 13:45:45	MarkDuplicates	Tracking 42408 as yet unmatched pairs. 42408 records in RAM.
INFO	2016-05-19 13:45:50	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,476
INFO	2016-05-19 13:45:50	MarkDuplicates	Tracking 13656 as yet unmatched pairs. 13656 records in RAM.
INFO	2016-05-19 13:45:53	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,775
INFO	2016-05-19 13:45:53	MarkDuplicates	Tracking 9036 as yet unmatched pairs. 9036 records in RAM.
INFO	2016-05-19 13:46:00	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    7s.  Last read position: chrM:14,342
INFO	2016-05-19 13:46:00	MarkDuplicates	Tracking 9468 as yet unmatched pairs. 9468 records in RAM.
INFO	2016-05-19 13:46:16	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:   15s.  Last read position: chrM:15,561
INFO	2016-05-19 13:46:16	MarkDuplicates	Tracking 32070 as yet unmatched pairs. 32070 records in RAM.
INFO	2016-05-19 13:46:20	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    4s.  Last read position: chrX:25,751,311
INFO	2016-05-19 13:46:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:46:25	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr10:51,668,586
INFO	2016-05-19 13:46:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:46:30	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr10:120,802,955
INFO	2016-05-19 13:46:30	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-19 13:46:35	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr11:55,157,103
INFO	2016-05-19 13:46:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:46:41	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr11:103,243,473
INFO	2016-05-19 13:46:41	MarkDuplicates	Tracking 52 as yet unmatched pairs. 52 records in RAM.
INFO	2016-05-19 13:46:45	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr12:64,041,873
INFO	2016-05-19 13:46:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:46:50	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:18,453,384
INFO	2016-05-19 13:46:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:46:54	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:89,914,851
INFO	2016-05-19 13:46:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:46:59	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:47,971,972
INFO	2016-05-19 13:46:59	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-19 13:47:04	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:111,045,187
INFO	2016-05-19 13:47:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:47:09	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr15:64,872,741
INFO	2016-05-19 13:47:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:47:16	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr16:21,150,015
INFO	2016-05-19 13:47:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:47:20	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr16:95,463,619
INFO	2016-05-19 13:47:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:47:24	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr17:64,364,676
INFO	2016-05-19 13:47:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:47:32	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr18:39,682,931
INFO	2016-05-19 13:47:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:47:36	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr19:5,072,789
INFO	2016-05-19 13:47:36	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-19 13:47:41	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:13,098,814
INFO	2016-05-19 13:47:41	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-19 13:47:45	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:88,208,152
INFO	2016-05-19 13:47:45	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-19 13:47:51	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr1:161,742,725
INFO	2016-05-19 13:47:51	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-19 13:47:55	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr2:28,525,586
INFO	2016-05-19 13:47:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:47:59	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr2:95,474,518
INFO	2016-05-19 13:47:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:48:03	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr2:157,367,577
INFO	2016-05-19 13:48:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:48:07	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr3:55,671,051
INFO	2016-05-19 13:48:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:48:11	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr3:122,158,999
INFO	2016-05-19 13:48:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:48:15	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr4:44,833,636
INFO	2016-05-19 13:48:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 13:48:19	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    3s.  Last read position: mm9_chr4:122,545,901
INFO	2016-05-19 13:48:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 13:48:27	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr5:31,454,607
INFO	2016-05-19 13:48:27	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-19 13:48:31	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr5:105,722,847
INFO	2016-05-19 13:48:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:48:44	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:   13s.  Last read position: mm9_chr6:7,724,397
INFO	2016-05-19 13:48:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:48:48	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:87,434,527
INFO	2016-05-19 13:48:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:48:52	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:149,079,737
INFO	2016-05-19 13:48:52	MarkDuplicates	Tracking 76 as yet unmatched pairs. 76 records in RAM.
INFO	2016-05-19 13:48:56	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr7:87,366,541
INFO	2016-05-19 13:48:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:49:00	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr7:148,020,920
INFO	2016-05-19 13:49:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:49:04	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr8:77,613,033
INFO	2016-05-19 13:49:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 13:49:08	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr9:11,120,207
INFO	2016-05-19 13:49:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 13:49:14	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr9:72,627,055
INFO	2016-05-19 13:49:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 13:49:18	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:114
INFO	2016-05-19 13:49:18	MarkDuplicates	Tracking 25480 as yet unmatched pairs. 25480 records in RAM.
INFO	2016-05-19 13:49:22	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:756
INFO	2016-05-19 13:49:22	MarkDuplicates	Tracking 54912 as yet unmatched pairs. 54912 records in RAM.
INFO	2016-05-19 13:49:25	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,460
INFO	2016-05-19 13:49:25	MarkDuplicates	Tracking 73520 as yet unmatched pairs. 73520 records in RAM.
INFO	2016-05-19 13:49:29	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,299
INFO	2016-05-19 13:49:29	MarkDuplicates	Tracking 50418 as yet unmatched pairs. 50418 records in RAM.
INFO	2016-05-19 13:49:33	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,929
INFO	2016-05-19 13:49:33	MarkDuplicates	Tracking 34976 as yet unmatched pairs. 34976 records in RAM.
INFO	2016-05-19 13:49:36	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:3,543
INFO	2016-05-19 13:49:36	MarkDuplicates	Tracking 51246 as yet unmatched pairs. 51246 records in RAM.
INFO	2016-05-19 13:49:40	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,148
INFO	2016-05-19 13:49:40	MarkDuplicates	Tracking 51792 as yet unmatched pairs. 51792 records in RAM.
INFO	2016-05-19 13:49:47	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:5,140
INFO	2016-05-19 13:49:47	MarkDuplicates	Tracking 27554 as yet unmatched pairs. 27554 records in RAM.
INFO	2016-05-19 13:49:52	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:6,255
INFO	2016-05-19 13:49:52	MarkDuplicates	Tracking 30126 as yet unmatched pairs. 30126 records in RAM.
INFO	2016-05-19 13:49:56	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,434
INFO	2016-05-19 13:49:56	MarkDuplicates	Tracking 39000 as yet unmatched pairs. 39000 records in RAM.
INFO	2016-05-19 13:49:59	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,177
INFO	2016-05-19 13:49:59	MarkDuplicates	Tracking 49588 as yet unmatched pairs. 49588 records in RAM.
INFO	2016-05-19 13:50:02	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,878
INFO	2016-05-19 13:50:02	MarkDuplicates	Tracking 33108 as yet unmatched pairs. 33108 records in RAM.
INFO	2016-05-19 13:50:06	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,757
INFO	2016-05-19 13:50:06	MarkDuplicates	Tracking 52302 as yet unmatched pairs. 52302 records in RAM.
INFO	2016-05-19 13:50:09	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,577
INFO	2016-05-19 13:50:09	MarkDuplicates	Tracking 35630 as yet unmatched pairs. 35630 records in RAM.
INFO	2016-05-19 13:50:12	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,339
INFO	2016-05-19 13:50:12	MarkDuplicates	Tracking 22896 as yet unmatched pairs. 22896 records in RAM.
INFO	2016-05-19 13:50:16	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrX:71,673,727
INFO	2016-05-19 13:50:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 13:50:18	MarkDuplicates	Read 82561520 records. 0 pairs never matched.
INFO	2016-05-19 13:50:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2928828848; totalMemory: 2956460032; maxMemory: 3817865216
INFO	2016-05-19 13:50:26	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-19 13:50:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-19 13:50:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-19 13:51:01	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-19 13:51:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1971662944; totalMemory: 2953314304; maxMemory: 3817865216
INFO	2016-05-19 13:51:03	MarkDuplicates	Marking 28517766 records as duplicates.
INFO	2016-05-19 13:51:03	MarkDuplicates	Found 4838909 optical duplicate clusters.
INFO	2016-05-19 13:52:43	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:39s.  Time for last 10,000,000:   99s.  Last read position: chr21:29,808,992
INFO	2016-05-19 13:54:26	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:22s.  Time for last 10,000,000:  102s.  Last read position: chr9:15,552,445
INFO	2016-05-19 13:55:53	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:49s.  Time for last 10,000,000:   87s.  Last read position: chrM:15,561
INFO	2016-05-19 13:57:38	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:34s.  Time for last 10,000,000:  104s.  Last read position: mm9_chr14:111,045,187
INFO	2016-05-19 13:59:24	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:19s.  Time for last 10,000,000:  105s.  Last read position: mm9_chr2:28,525,586
INFO	2016-05-19 14:01:11	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:06s.  Time for last 10,000,000:  106s.  Last read position: mm9_chr6:87,434,527
INFO	2016-05-19 14:02:50	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:11:46s.  Time for last 10,000,000:   99s.  Last read position: mm9_chrM:2,299
INFO	2016-05-19 14:04:16	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:13:12s.  Time for last 10,000,000:   85s.  Last read position: mm9_chrM:14,577
INFO	2016-05-19 14:04:40	MarkDuplicates	Before output close freeMemory: 3005123040; totalMemory: 3035627520; maxMemory: 3817865216
INFO	2016-05-19 14:04:40	MarkDuplicates	After output close freeMemory: 3005121984; totalMemory: 3035627520; maxMemory: 3817865216
[Thu May 19 14:04:40 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 21.45 minutes.
Runtime.totalMemory()=3035627520
[bam_sort_core] merging from 34 files...

Num	4
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9
Name	dedup_bam_PE rep2
Thread	thread_21
PID	12936

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

Start	2016-05-19 13:36:43
End	2016-05-19 18:26:47
Elapsed	04:50:03
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.PE2SE.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

 samtools fixmate -r /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam

   
--------------------Stdout--------------------



 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 49 files...
[bam_sort_core] merging from 49 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu May 19 15:49:05 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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
[Thu May 19 15:49:05 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	2016-05-19 15:49:06	MarkDuplicates	Start of doWork freeMemory: 254891160; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-19 15:49:06	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-19 15:49:06	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-19 15:49:19	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:   12s.  Last read position: chr11:69,490,098
INFO	2016-05-19 15:49:19	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-19 15:49:31	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:   12s.  Last read position: chr12:124,530,937
INFO	2016-05-19 15:49:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:49:42	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:   11s.  Last read position: chr15:51,481,093
INFO	2016-05-19 15:49:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:49:52	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    9s.  Last read position: chr17:61,851,101
INFO	2016-05-19 15:49:52	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-19 15:49:59	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    6s.  Last read position: chr1:12,540,773
INFO	2016-05-19 15:49:59	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-19 15:50:06	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    7s.  Last read position: chr1:209,222,510
INFO	2016-05-19 15:50:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:50:13	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    6s.  Last read position: chr2:24,677,523
INFO	2016-05-19 15:50:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:50:22	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    8s.  Last read position: chr2:226,267,866
INFO	2016-05-19 15:50:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:50:28	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    6s.  Last read position: chr3:170,883,868
INFO	2016-05-19 15:50:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:50:39	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:   11s.  Last read position: chr5:10,551,435
INFO	2016-05-19 15:50:39	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-19 15:50:45	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    6s.  Last read position: chr6:29,141,233
INFO	2016-05-19 15:50:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:50:52	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    7s.  Last read position: chr7:86,321,498
INFO	2016-05-19 15:50:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:51:03	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:   10s.  Last read position: chr8:141,601,520
INFO	2016-05-19 15:51:03	MarkDuplicates	Tracking 18 as yet unmatched pairs. 18 records in RAM.
INFO	2016-05-19 15:51:10	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    6s.  Last read position: chrM:209
INFO	2016-05-19 15:51:10	MarkDuplicates	Tracking 20016 as yet unmatched pairs. 20016 records in RAM.
INFO	2016-05-19 15:51:28	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:   18s.  Last read position: chrM:1,022
INFO	2016-05-19 15:51:28	MarkDuplicates	Tracking 15990 as yet unmatched pairs. 15990 records in RAM.
INFO	2016-05-19 15:51:36	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    7s.  Last read position: chrM:1,740
INFO	2016-05-19 15:51:36	MarkDuplicates	Tracking 35100 as yet unmatched pairs. 35100 records in RAM.
INFO	2016-05-19 15:51:41	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,530
INFO	2016-05-19 15:51:41	MarkDuplicates	Tracking 14658 as yet unmatched pairs. 14658 records in RAM.
INFO	2016-05-19 15:51:46	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,856
INFO	2016-05-19 15:51:46	MarkDuplicates	Tracking 85242 as yet unmatched pairs. 85242 records in RAM.
INFO	2016-05-19 15:51:53	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,215
INFO	2016-05-19 15:51:53	MarkDuplicates	Tracking 97812 as yet unmatched pairs. 97812 records in RAM.
INFO	2016-05-19 15:51:58	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,467
INFO	2016-05-19 15:51:58	MarkDuplicates	Tracking 26100 as yet unmatched pairs. 26100 records in RAM.
INFO	2016-05-19 15:52:03	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,784
INFO	2016-05-19 15:52:03	MarkDuplicates	Tracking 57246 as yet unmatched pairs. 57246 records in RAM.
INFO	2016-05-19 15:52:12	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    8s.  Last read position: chrM:4,784
INFO	2016-05-19 15:52:12	MarkDuplicates	Tracking 4270 as yet unmatched pairs. 4270 records in RAM.
INFO	2016-05-19 15:52:17	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    4s.  Last read position: chrM:5,817
INFO	2016-05-19 15:52:17	MarkDuplicates	Tracking 8822 as yet unmatched pairs. 8822 records in RAM.
INFO	2016-05-19 15:52:22	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,481
INFO	2016-05-19 15:52:22	MarkDuplicates	Tracking 23338 as yet unmatched pairs. 23338 records in RAM.
INFO	2016-05-19 15:52:27	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,218
INFO	2016-05-19 15:52:27	MarkDuplicates	Tracking 14896 as yet unmatched pairs. 14896 records in RAM.
INFO	2016-05-19 15:52:36	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    9s.  Last read position: chrM:8,022
INFO	2016-05-19 15:52:36	MarkDuplicates	Tracking 14200 as yet unmatched pairs. 14200 records in RAM.
INFO	2016-05-19 15:52:41	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    4s.  Last read position: chrM:9,148
INFO	2016-05-19 15:52:41	MarkDuplicates	Tracking 20796 as yet unmatched pairs. 20796 records in RAM.
INFO	2016-05-19 15:52:47	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,825
INFO	2016-05-19 15:52:47	MarkDuplicates	Tracking 72578 as yet unmatched pairs. 72578 records in RAM.
INFO	2016-05-19 15:52:54	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    6s.  Last read position: chrM:10,184
INFO	2016-05-19 15:52:54	MarkDuplicates	Tracking 37126 as yet unmatched pairs. 37126 records in RAM.
INFO	2016-05-19 15:53:18	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:   24s.  Last read position: chrM:10,631
INFO	2016-05-19 15:53:18	MarkDuplicates	Tracking 38772 as yet unmatched pairs. 38772 records in RAM.
INFO	2016-05-19 15:53:25	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    7s.  Last read position: chrM:11,312
INFO	2016-05-19 15:53:25	MarkDuplicates	Tracking 47576 as yet unmatched pairs. 47576 records in RAM.
INFO	2016-05-19 15:53:32	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,838
INFO	2016-05-19 15:53:32	MarkDuplicates	Tracking 8624 as yet unmatched pairs. 8624 records in RAM.
INFO	2016-05-19 15:53:37	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,246
INFO	2016-05-19 15:53:37	MarkDuplicates	Tracking 48316 as yet unmatched pairs. 48316 records in RAM.
INFO	2016-05-19 15:53:45	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,619
INFO	2016-05-19 15:53:45	MarkDuplicates	Tracking 54144 as yet unmatched pairs. 54144 records in RAM.
INFO	2016-05-19 15:53:50	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,108
INFO	2016-05-19 15:53:50	MarkDuplicates	Tracking 22746 as yet unmatched pairs. 22746 records in RAM.
INFO	2016-05-19 15:53:54	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,647
INFO	2016-05-19 15:53:54	MarkDuplicates	Tracking 13160 as yet unmatched pairs. 13160 records in RAM.
INFO	2016-05-19 15:53:59	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,058
INFO	2016-05-19 15:53:59	MarkDuplicates	Tracking 34014 as yet unmatched pairs. 34014 records in RAM.
INFO	2016-05-19 15:54:06	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    6s.  Last read position: chrM:14,833
INFO	2016-05-19 15:54:06	MarkDuplicates	Tracking 11308 as yet unmatched pairs. 11308 records in RAM.
INFO	2016-05-19 15:54:10	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,144
INFO	2016-05-19 15:54:10	MarkDuplicates	Tracking 59596 as yet unmatched pairs. 59596 records in RAM.
INFO	2016-05-19 15:54:17	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    6s.  Last read position: chrM:15,469
INFO	2016-05-19 15:54:17	MarkDuplicates	Tracking 25988 as yet unmatched pairs. 25988 records in RAM.
INFO	2016-05-19 15:54:22	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,760
INFO	2016-05-19 15:54:22	MarkDuplicates	Tracking 42096 as yet unmatched pairs. 42096 records in RAM.
INFO	2016-05-19 15:54:27	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    5s.  Last read position: chrM:16,192
INFO	2016-05-19 15:54:27	MarkDuplicates	Tracking 21338 as yet unmatched pairs. 21338 records in RAM.
INFO	2016-05-19 15:54:35	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    7s.  Last read position: chrX:38,314,713
INFO	2016-05-19 15:54:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:54:41	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:35s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr10:69,934,290
INFO	2016-05-19 15:54:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:54:54	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:   12s.  Last read position: mm9_chr11:5,724,943
INFO	2016-05-19 15:54:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:55:01	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr11:80,801,683
INFO	2016-05-19 15:55:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:55:08	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:06:01s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr12:40,957,819
INFO	2016-05-19 15:55:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:55:17	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    9s.  Last read position: mm9_chr13:4,608,222
INFO	2016-05-19 15:55:17	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-19 15:55:22	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr13:95,725,986
INFO	2016-05-19 15:55:22	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-19 15:55:28	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr14:68,370,931
INFO	2016-05-19 15:55:28	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 15:55:33	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr15:51,128,671
INFO	2016-05-19 15:55:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:55:38	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr16:23,233,726
INFO	2016-05-19 15:55:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:55:46	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    8s.  Last read position: mm9_chr17:22,870,751
INFO	2016-05-19 15:55:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:55:53	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr17:91,785,337
INFO	2016-05-19 15:55:53	MarkDuplicates	Tracking 22 as yet unmatched pairs. 22 records in RAM.
INFO	2016-05-19 15:56:00	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr19:3,369,195
INFO	2016-05-19 15:56:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:56:07	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr1:24,619,938
INFO	2016-05-19 15:56:07	MarkDuplicates	Tracking 12236 as yet unmatched pairs. 12236 records in RAM.
INFO	2016-05-19 15:56:12	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr1:120,767,392
INFO	2016-05-19 15:56:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:56:18	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr1:193,583,055
INFO	2016-05-19 15:56:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 15:56:45	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:07:39s.  Time for last 1,000,000:   26s.  Last read position: mm9_chr2:78,999,609
INFO	2016-05-19 15:56:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:56:51	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr2:153,190,361
INFO	2016-05-19 15:56:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:56:58	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr3:66,163,154
INFO	2016-05-19 15:56:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:57:05	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr3:143,155,645
INFO	2016-05-19 15:57:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:57:12	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr4:86,876,432
INFO	2016-05-19 15:57:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-19 15:57:18	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:08:12s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr5:3,873,581
INFO	2016-05-19 15:57:18	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-19 15:57:27	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    8s.  Last read position: mm9_chr5:100,405,923
INFO	2016-05-19 15:57:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:57:32	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:08:26s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr6:16,835,569
INFO	2016-05-19 15:57:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:57:38	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr6:108,015,102
INFO	2016-05-19 15:57:38	MarkDuplicates	Tracking 56 as yet unmatched pairs. 56 records in RAM.
INFO	2016-05-19 15:57:43	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr7:36,620,873
INFO	2016-05-19 15:57:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:57:49	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr7:129,306,337
INFO	2016-05-19 15:57:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:57:54	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr8:72,240,954
INFO	2016-05-19 15:57:54	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-19 15:58:03	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:08:57s.  Time for last 1,000,000:    9s.  Last read position: mm9_chr9:14,090,048
INFO	2016-05-19 15:58:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-19 15:58:09	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr9:93,266,546
INFO	2016-05-19 15:58:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-19 15:58:15	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:09:08s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:126
INFO	2016-05-19 15:58:15	MarkDuplicates	Tracking 91154 as yet unmatched pairs. 91154 records in RAM.
INFO	2016-05-19 15:58:27	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:   12s.  Last read position: mm9_chrM:321
INFO	2016-05-19 15:58:27	MarkDuplicates	Tracking 138512 as yet unmatched pairs. 138512 records in RAM.
INFO	2016-05-19 15:58:34	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:09:27s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:546
INFO	2016-05-19 15:58:34	MarkDuplicates	Tracking 54062 as yet unmatched pairs. 54062 records in RAM.
INFO	2016-05-19 15:58:42	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:751
INFO	2016-05-19 15:58:42	MarkDuplicates	Tracking 96466 as yet unmatched pairs. 96466 records in RAM.
INFO	2016-05-19 15:58:50	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:09:44s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:961
INFO	2016-05-19 15:58:50	MarkDuplicates	Tracking 76662 as yet unmatched pairs. 76662 records in RAM.
INFO	2016-05-19 15:59:01	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:09:54s.  Time for last 1,000,000:   10s.  Last read position: mm9_chrM:1,139
INFO	2016-05-19 15:59:01	MarkDuplicates	Tracking 104396 as yet unmatched pairs. 104396 records in RAM.
INFO	2016-05-19 15:59:06	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:10:00s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:1,376
INFO	2016-05-19 15:59:06	MarkDuplicates	Tracking 72284 as yet unmatched pairs. 72284 records in RAM.
INFO	2016-05-19 15:59:12	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:1,735
INFO	2016-05-19 15:59:12	MarkDuplicates	Tracking 59004 as yet unmatched pairs. 59004 records in RAM.
INFO	2016-05-19 15:59:17	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:10:10s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:2,012
INFO	2016-05-19 15:59:17	MarkDuplicates	Tracking 42852 as yet unmatched pairs. 42852 records in RAM.
INFO	2016-05-19 15:59:22	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:10:15s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:2,264
INFO	2016-05-19 15:59:22	MarkDuplicates	Tracking 128380 as yet unmatched pairs. 128380 records in RAM.
INFO	2016-05-19 15:59:27	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:2,511
INFO	2016-05-19 15:59:27	MarkDuplicates	Tracking 91186 as yet unmatched pairs. 91186 records in RAM.
INFO	2016-05-19 15:59:32	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:10:25s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:2,716
INFO	2016-05-19 15:59:32	MarkDuplicates	Tracking 61940 as yet unmatched pairs. 61940 records in RAM.
INFO	2016-05-19 15:59:42	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    9s.  Last read position: mm9_chrM:2,891
INFO	2016-05-19 15:59:42	MarkDuplicates	Tracking 91070 as yet unmatched pairs. 91070 records in RAM.
INFO	2016-05-19 15:59:50	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:10:43s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:3,088
INFO	2016-05-19 15:59:50	MarkDuplicates	Tracking 82062 as yet unmatched pairs. 82062 records in RAM.
INFO	2016-05-19 15:59:58	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:3,284
INFO	2016-05-19 15:59:58	MarkDuplicates	Tracking 48486 as yet unmatched pairs. 48486 records in RAM.
INFO	2016-05-19 16:00:06	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:10:59s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:3,483
INFO	2016-05-19 16:00:06	MarkDuplicates	Tracking 108212 as yet unmatched pairs. 108212 records in RAM.
INFO	2016-05-19 16:00:32	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:11:26s.  Time for last 1,000,000:   26s.  Last read position: mm9_chrM:3,644
INFO	2016-05-19 16:00:32	MarkDuplicates	Tracking 84830 as yet unmatched pairs. 84830 records in RAM.
INFO	2016-05-19 16:00:40	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:11:33s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:3,845
INFO	2016-05-19 16:00:40	MarkDuplicates	Tracking 83514 as yet unmatched pairs. 83514 records in RAM.
INFO	2016-05-19 16:00:49	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:11:43s.  Time for last 1,000,000:    9s.  Last read position: mm9_chrM:4,035
INFO	2016-05-19 16:00:49	MarkDuplicates	Tracking 120424 as yet unmatched pairs. 120424 records in RAM.
INFO	2016-05-19 16:01:02	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:11:55s.  Time for last 1,000,000:   12s.  Last read position: mm9_chrM:4,222
INFO	2016-05-19 16:01:02	MarkDuplicates	Tracking 64188 as yet unmatched pairs. 64188 records in RAM.
INFO	2016-05-19 16:01:09	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:12:02s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:4,437
INFO	2016-05-19 16:01:09	MarkDuplicates	Tracking 87854 as yet unmatched pairs. 87854 records in RAM.
INFO	2016-05-19 16:01:17	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:12:10s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:4,695
INFO	2016-05-19 16:01:17	MarkDuplicates	Tracking 103592 as yet unmatched pairs. 103592 records in RAM.
INFO	2016-05-19 16:01:24	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:12:17s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:5,349
INFO	2016-05-19 16:01:24	MarkDuplicates	Tracking 35952 as yet unmatched pairs. 35952 records in RAM.
INFO	2016-05-19 16:01:31	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:12:24s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:5,782
INFO	2016-05-19 16:01:31	MarkDuplicates	Tracking 61986 as yet unmatched pairs. 61986 records in RAM.
INFO	2016-05-19 16:01:38	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:12:31s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:6,102
INFO	2016-05-19 16:01:38	MarkDuplicates	Tracking 57040 as yet unmatched pairs. 57040 records in RAM.
INFO	2016-05-19 16:01:45	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:12:38s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:6,392
INFO	2016-05-19 16:01:45	MarkDuplicates	Tracking 37268 as yet unmatched pairs. 37268 records in RAM.
INFO	2016-05-19 16:01:52	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:12:46s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:11,131
INFO	2016-05-19 16:01:52	MarkDuplicates	Tracking 49800 as yet unmatched pairs. 49800 records in RAM.
INFO	2016-05-19 16:02:05	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:12:58s.  Time for last 1,000,000:   12s.  Last read position: mm9_chrM:11,303
INFO	2016-05-19 16:02:05	MarkDuplicates	Tracking 170126 as yet unmatched pairs. 170126 records in RAM.
INFO	2016-05-19 16:02:14	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:13:07s.  Time for last 1,000,000:    9s.  Last read position: mm9_chrM:11,510
INFO	2016-05-19 16:02:14	MarkDuplicates	Tracking 105448 as yet unmatched pairs. 105448 records in RAM.
INFO	2016-05-19 16:02:22	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:13:16s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:11,777
INFO	2016-05-19 16:02:22	MarkDuplicates	Tracking 66180 as yet unmatched pairs. 66180 records in RAM.
INFO	2016-05-19 16:02:39	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:13:32s.  Time for last 1,000,000:   16s.  Last read position: mm9_chrM:11,992
INFO	2016-05-19 16:02:39	MarkDuplicates	Tracking 116982 as yet unmatched pairs. 116982 records in RAM.
INFO	2016-05-19 16:02:47	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:13:40s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:12,169
INFO	2016-05-19 16:02:47	MarkDuplicates	Tracking 73604 as yet unmatched pairs. 73604 records in RAM.
INFO	2016-05-19 16:02:55	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:13:49s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:12,379
INFO	2016-05-19 16:02:55	MarkDuplicates	Tracking 75236 as yet unmatched pairs. 75236 records in RAM.
INFO	2016-05-19 16:03:03	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:13:56s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:12,653
INFO	2016-05-19 16:03:03	MarkDuplicates	Tracking 59878 as yet unmatched pairs. 59878 records in RAM.
INFO	2016-05-19 16:03:11	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:14:04s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:12,909
INFO	2016-05-19 16:03:11	MarkDuplicates	Tracking 31888 as yet unmatched pairs. 31888 records in RAM.
INFO	2016-05-19 16:03:23	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:14:16s.  Time for last 1,000,000:   11s.  Last read position: mm9_chrM:13,289
INFO	2016-05-19 16:03:23	MarkDuplicates	Tracking 55572 as yet unmatched pairs. 55572 records in RAM.
INFO	2016-05-19 16:03:29	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:14:23s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:13,543
INFO	2016-05-19 16:03:29	MarkDuplicates	Tracking 79548 as yet unmatched pairs. 79548 records in RAM.
INFO	2016-05-19 16:03:36	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:14:30s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:13,786
INFO	2016-05-19 16:03:36	MarkDuplicates	Tracking 57270 as yet unmatched pairs. 57270 records in RAM.
INFO	2016-05-19 16:03:43	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:14:36s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:14,188
INFO	2016-05-19 16:03:43	MarkDuplicates	Tracking 21596 as yet unmatched pairs. 21596 records in RAM.
INFO	2016-05-19 16:03:50	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:14:43s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:14,401
INFO	2016-05-19 16:03:50	MarkDuplicates	Tracking 69180 as yet unmatched pairs. 69180 records in RAM.
INFO	2016-05-19 16:03:57	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:14:50s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:14,619
INFO	2016-05-19 16:03:57	MarkDuplicates	Tracking 62872 as yet unmatched pairs. 62872 records in RAM.
INFO	2016-05-19 16:04:04	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:14:58s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:14,838
INFO	2016-05-19 16:04:04	MarkDuplicates	Tracking 78926 as yet unmatched pairs. 78926 records in RAM.
INFO	2016-05-19 16:04:12	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:15:05s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:15,131
INFO	2016-05-19 16:04:12	MarkDuplicates	Tracking 35832 as yet unmatched pairs. 35832 records in RAM.
INFO	2016-05-19 16:04:26	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:15:19s.  Time for last 1,000,000:   14s.  Last read position: mm9_chrM:15,375
INFO	2016-05-19 16:04:26	MarkDuplicates	Tracking 59084 as yet unmatched pairs. 59084 records in RAM.
INFO	2016-05-19 16:04:35	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:15:28s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:15,591
INFO	2016-05-19 16:04:35	MarkDuplicates	Tracking 68446 as yet unmatched pairs. 68446 records in RAM.
INFO	2016-05-19 16:05:09	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:16:02s.  Time for last 1,000,000:   34s.  Last read position: mm9_chrM:16,201
INFO	2016-05-19 16:05:09	MarkDuplicates	Tracking 32188 as yet unmatched pairs. 32188 records in RAM.
INFO	2016-05-19 16:05:16	MarkDuplicates	Read 118771168 records. 0 pairs never matched.
INFO	2016-05-19 16:05:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4000912720; totalMemory: 4027580416; maxMemory: 4027580416
INFO	2016-05-19 16:05:17	MarkDuplicates	Will retain up to 125861888 duplicate indices before spilling to disk.
INFO	2016-05-19 16:05:18	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-19 16:06:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-19 16:07:36	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-19 16:07:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2952499968; totalMemory: 3986685952; maxMemory: 3986685952
INFO	2016-05-19 16:07:44	MarkDuplicates	Marking 73821852 records as duplicates.
INFO	2016-05-19 16:07:44	MarkDuplicates	Found 22831091 optical duplicate clusters.
INFO	2016-05-19 16:11:07	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:03:22s.  Time for last 10,000,000:  202s.  Last read position: chr5:10,551,435
INFO	2016-05-19 16:14:07	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:06:22s.  Time for last 10,000,000:  179s.  Last read position: chrM:3,467
INFO	2016-05-19 16:16:53	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:09:08s.  Time for last 10,000,000:  166s.  Last read position: chrM:10,631
INFO	2016-05-19 16:19:41	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:11:56s.  Time for last 10,000,000:  168s.  Last read position: chrM:15,469
INFO	2016-05-19 16:22:55	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:15:10s.  Time for last 10,000,000:  193s.  Last read position: mm9_chr14:68,370,931
INFO	2016-05-19 16:26:19	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:18:34s.  Time for last 10,000,000:  204s.  Last read position: mm9_chr2:153,190,361
INFO	2016-05-19 16:29:45	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:22:00s.  Time for last 10,000,000:  205s.  Last read position: mm9_chr8:72,240,954
INFO	2016-05-19 16:32:42	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:24:57s.  Time for last 10,000,000:  176s.  Last read position: mm9_chrM:1,735
INFO	2016-05-19 16:35:34	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:27:49s.  Time for last 10,000,000:  172s.  Last read position: mm9_chrM:3,845
INFO	2016-05-19 16:38:20	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:30:35s.  Time for last 10,000,000:  165s.  Last read position: mm9_chrM:11,303
INFO	2016-05-19 16:41:10	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:33:26s.  Time for last 10,000,000:  170s.  Last read position: mm9_chrM:13,786
INFO	2016-05-19 16:43:36	MarkDuplicates	Before output close freeMemory: 4098618896; totalMemory: 4128768000; maxMemory: 4128768000
INFO	2016-05-19 16:43:36	MarkDuplicates	After output close freeMemory: 4098617840; totalMemory: 4128768000; maxMemory: 4128768000
[Thu May 19 16:43:37 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 54.52 minutes.
Runtime.totalMemory()=4128768000
[bam_sort_core] merging from 49 files...

Num	5
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_10
Name	nmsrt_bam rep1
Thread	thread_20
PID	42748

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

Start	2016-05-19 15:08:11
End	2016-05-19 15:35:15
Elapsed	00:27:04
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.PE2SE.nodup.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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 23 files...

Num	6
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_11
Name	bam_to_bedpe rep1
Thread	thread_20
PID	3904

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

Start	2016-05-19 15:35:16
End	2016-05-19 15:38:27
Elapsed	00:03:11
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.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	5488

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

Start	2016-05-19 15:38:29
End	2016-05-19 15:41:28
Elapsed	00:02:59
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.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	7165

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

Start	2016-05-19 15:41:29
End	2016-05-19 15:45:11
Elapsed	00:03:41
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.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.00" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.01" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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	7977

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

Start	2016-05-19 15:45:11
End	2016-05-19 15:47:00
Elapsed	00:01:49
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.PE2SE.nodup.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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	7979

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

Start	2016-05-19 15:45:12
End	2016-05-19 15:46:09
Elapsed	00:00:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	7990

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

Start	2016-05-19 15:45:12
End	2016-05-19 15:46:09
Elapsed	00:00:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	9634

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

Start	2016-05-19 15:47:01
End	2016-05-19 15:49:04
Elapsed	00:02:02
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.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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	10046

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

Start	2016-05-19 15:49:04
End	2016-05-19 16:52:40
Elapsed	01:03:35
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.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmpnp5LBQ/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign28937bf3dc5e
done. read 25000000 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1419964 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.226889522194291 
Top 3 estimates for fragment length 0 
Window half size 430 
Phantom peak location 80 
Phantom peak Correlation 0.2473714 
Normalized Strand cross-correlation coefficient (NSC) 1.597854 
Relative Strand Cross correlation Coefficient (RSC) 0.8056284 
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	10054

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

Start	2016-05-19 15:49:04
End	2016-05-19 16:10:09
Elapsed	00:21:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:49:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:49:15:  1000000 
INFO  @ Thu, 19 May 2016 15:49:17:  2000000 
INFO  @ Thu, 19 May 2016 15:49:19:  3000000 
INFO  @ Thu, 19 May 2016 15:49:22:  4000000 
INFO  @ Thu, 19 May 2016 15:49:24:  5000000 
INFO  @ Thu, 19 May 2016 15:49:26:  6000000 
INFO  @ Thu, 19 May 2016 15:49:29:  7000000 
INFO  @ Thu, 19 May 2016 15:49:31:  8000000 
INFO  @ Thu, 19 May 2016 15:49:34:  9000000 
INFO  @ Thu, 19 May 2016 15:49:36:  10000000 
INFO  @ Thu, 19 May 2016 15:49:38:  11000000 
INFO  @ Thu, 19 May 2016 15:49:41:  12000000 
INFO  @ Thu, 19 May 2016 15:49:43:  13000000 
INFO  @ Thu, 19 May 2016 15:49:45:  14000000 
INFO  @ Thu, 19 May 2016 15:49:48:  15000000 
INFO  @ Thu, 19 May 2016 15:49:50:  16000000 
INFO  @ Thu, 19 May 2016 15:49:53:  17000000 
INFO  @ Thu, 19 May 2016 15:49:55:  18000000 
INFO  @ Thu, 19 May 2016 15:49:57:  19000000 
INFO  @ Thu, 19 May 2016 15:50:00:  20000000 
INFO  @ Thu, 19 May 2016 15:50:02:  21000000 
INFO  @ Thu, 19 May 2016 15:50:04:  22000000 
INFO  @ Thu, 19 May 2016 15:50:07:  23000000 
INFO  @ Thu, 19 May 2016 15:50:09:  24000000 
INFO  @ Thu, 19 May 2016 15:50:12:  25000000 
INFO  @ Thu, 19 May 2016 15:50:14:  26000000 
INFO  @ Thu, 19 May 2016 15:50:17:  27000000 
INFO  @ Thu, 19 May 2016 15:50:19: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 15:50:19: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 15:50:19: #1  total tags in treatment: 27021878 
INFO  @ Thu, 19 May 2016 15:50:19: #1 finished! 
INFO  @ Thu, 19 May 2016 15:50:19: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:50:19: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:50:19: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:50:19: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:50:19: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:50:19: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 15:50:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 15:51:52: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 15:54:16: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 15:54:21: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 15:54:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 15:54:27: Done! 
INFO  @ Thu, 19 May 2016 15:54:45: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:54:45: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:54:45: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:54:47:  1000000 
INFO  @ Thu, 19 May 2016 15:54:50:  2000000 
INFO  @ Thu, 19 May 2016 15:54:52:  3000000 
INFO  @ Thu, 19 May 2016 15:54:54:  4000000 
INFO  @ Thu, 19 May 2016 15:54:57:  5000000 
INFO  @ Thu, 19 May 2016 15:54:59:  6000000 
INFO  @ Thu, 19 May 2016 15:55:01:  7000000 
INFO  @ Thu, 19 May 2016 15:55:04:  8000000 
INFO  @ Thu, 19 May 2016 15:55:06:  9000000 
INFO  @ Thu, 19 May 2016 15:55:09:  10000000 
INFO  @ Thu, 19 May 2016 15:55:11:  11000000 
INFO  @ Thu, 19 May 2016 15:55:13:  12000000 
INFO  @ Thu, 19 May 2016 15:55:16:  13000000 
INFO  @ Thu, 19 May 2016 15:55:18:  14000000 
INFO  @ Thu, 19 May 2016 15:55:21:  15000000 
INFO  @ Thu, 19 May 2016 15:55:23:  16000000 
INFO  @ Thu, 19 May 2016 15:55:25:  17000000 
INFO  @ Thu, 19 May 2016 15:55:28:  18000000 
INFO  @ Thu, 19 May 2016 15:55:30:  19000000 
INFO  @ Thu, 19 May 2016 15:55:33:  20000000 
INFO  @ Thu, 19 May 2016 15:55:35:  21000000 
INFO  @ Thu, 19 May 2016 15:55:37:  22000000 
INFO  @ Thu, 19 May 2016 15:55:39:  23000000 
INFO  @ Thu, 19 May 2016 15:55:42:  24000000 
INFO  @ Thu, 19 May 2016 15:55:44:  25000000 
INFO  @ Thu, 19 May 2016 15:55:46:  26000000 
INFO  @ Thu, 19 May 2016 15:55:49:  27000000 
INFO  @ Thu, 19 May 2016 15:55:51: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 15:55:51: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 15:55:51: #1  total tags in treatment: 27021878 
INFO  @ Thu, 19 May 2016 15:55:51: #1 finished! 
INFO  @ Thu, 19 May 2016 15:55:51: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:55:51: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:55:51: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:55:51: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:55:51: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:55:51: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 15:55:51: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 15:55:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 15:57:26: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 15:57:26: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 15:57:26: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 15:57:26: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 15:57:26: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 16:09:30: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 16:09:43: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 16:09:51: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 16:09:57: 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	10065

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

Start	2016-05-19 15:49:05
End	2016-05-19 16:10:06
Elapsed	00:21:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:49:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:49:15:  1000000 
INFO  @ Thu, 19 May 2016 15:49:17:  2000000 
INFO  @ Thu, 19 May 2016 15:49:19:  3000000 
INFO  @ Thu, 19 May 2016 15:49:21:  4000000 
INFO  @ Thu, 19 May 2016 15:49:24:  5000000 
INFO  @ Thu, 19 May 2016 15:49:26:  6000000 
INFO  @ Thu, 19 May 2016 15:49:29:  7000000 
INFO  @ Thu, 19 May 2016 15:49:31:  8000000 
INFO  @ Thu, 19 May 2016 15:49:33:  9000000 
INFO  @ Thu, 19 May 2016 15:49:35:  10000000 
INFO  @ Thu, 19 May 2016 15:49:38:  11000000 
INFO  @ Thu, 19 May 2016 15:49:40:  12000000 
INFO  @ Thu, 19 May 2016 15:49:42:  13000000 
INFO  @ Thu, 19 May 2016 15:49:45:  14000000 
INFO  @ Thu, 19 May 2016 15:49:47:  15000000 
INFO  @ Thu, 19 May 2016 15:49:49:  16000000 
INFO  @ Thu, 19 May 2016 15:49:52:  17000000 
INFO  @ Thu, 19 May 2016 15:49:54:  18000000 
INFO  @ Thu, 19 May 2016 15:49:57:  19000000 
INFO  @ Thu, 19 May 2016 15:49:59:  20000000 
INFO  @ Thu, 19 May 2016 15:50:01:  21000000 
INFO  @ Thu, 19 May 2016 15:50:03:  22000000 
INFO  @ Thu, 19 May 2016 15:50:06:  23000000 
INFO  @ Thu, 19 May 2016 15:50:08:  24000000 
INFO  @ Thu, 19 May 2016 15:50:11:  25000000 
INFO  @ Thu, 19 May 2016 15:50:13:  26000000 
INFO  @ Thu, 19 May 2016 15:50:16:  27000000 
INFO  @ Thu, 19 May 2016 15:50:18: #1 tag size is determined as 63 bps 
INFO  @ Thu, 19 May 2016 15:50:18: #1 tag size = 63 
INFO  @ Thu, 19 May 2016 15:50:18: #1  total tags in treatment: 27021876 
INFO  @ Thu, 19 May 2016 15:50:18: #1 finished! 
INFO  @ Thu, 19 May 2016 15:50:18: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:50:18: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:50:18: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:50:18: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:50:18: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:50:18: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 15:50:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 15:51:52: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 15:54:19: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 15:54:24: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 15:54:27: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 15:54:30: Done! 
INFO  @ Thu, 19 May 2016 15:54:46: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:54:46: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:54:46: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:54:48:  1000000 
INFO  @ Thu, 19 May 2016 15:54:51:  2000000 
INFO  @ Thu, 19 May 2016 15:54:53:  3000000 
INFO  @ Thu, 19 May 2016 15:54:55:  4000000 
INFO  @ Thu, 19 May 2016 15:54:58:  5000000 
INFO  @ Thu, 19 May 2016 15:55:00:  6000000 
INFO  @ Thu, 19 May 2016 15:55:03:  7000000 
INFO  @ Thu, 19 May 2016 15:55:05:  8000000 
INFO  @ Thu, 19 May 2016 15:55:07:  9000000 
INFO  @ Thu, 19 May 2016 15:55:10:  10000000 
INFO  @ Thu, 19 May 2016 15:55:13:  11000000 
INFO  @ Thu, 19 May 2016 15:55:15:  12000000 
INFO  @ Thu, 19 May 2016 15:55:18:  13000000 
INFO  @ Thu, 19 May 2016 15:55:20:  14000000 
INFO  @ Thu, 19 May 2016 15:55:23:  15000000 
INFO  @ Thu, 19 May 2016 15:55:25:  16000000 
INFO  @ Thu, 19 May 2016 15:55:27:  17000000 
INFO  @ Thu, 19 May 2016 15:55:30:  18000000 
INFO  @ Thu, 19 May 2016 15:55:32:  19000000 
INFO  @ Thu, 19 May 2016 15:55:35:  20000000 
INFO  @ Thu, 19 May 2016 15:55:37:  21000000 
INFO  @ Thu, 19 May 2016 15:55:40:  22000000 
INFO  @ Thu, 19 May 2016 15:55:42:  23000000 
INFO  @ Thu, 19 May 2016 15:55:45:  24000000 
INFO  @ Thu, 19 May 2016 15:55:47:  25000000 
INFO  @ Thu, 19 May 2016 15:55:50:  26000000 
INFO  @ Thu, 19 May 2016 15:55:52:  27000000 
INFO  @ Thu, 19 May 2016 15:55:54: #1 tag size is determined as 63 bps 
INFO  @ Thu, 19 May 2016 15:55:54: #1 tag size = 63 
INFO  @ Thu, 19 May 2016 15:55:54: #1  total tags in treatment: 27021876 
INFO  @ Thu, 19 May 2016 15:55:54: #1 finished! 
INFO  @ Thu, 19 May 2016 15:55:54: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:55:54: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:55:54: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:55:54: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:55:54: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:55:54: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 15:55:54: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 15:55:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 15:57:30: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 15:57:30: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 15:57:30: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 15:57:30: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 15:57:30: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 16:09:25: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 16:09:38: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 16:09:47: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 16:09:53: 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	10068

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

Start	2016-05-19 15:49:05
End	2016-05-19 16:17:31
Elapsed	00:28:25
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.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:49:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:49:14:  1000000 
INFO  @ Thu, 19 May 2016 15:49:16:  2000000 
INFO  @ Thu, 19 May 2016 15:49:18:  3000000 
INFO  @ Thu, 19 May 2016 15:49:20:  4000000 
INFO  @ Thu, 19 May 2016 15:49:23:  5000000 
INFO  @ Thu, 19 May 2016 15:49:25:  6000000 
INFO  @ Thu, 19 May 2016 15:49:27:  7000000 
INFO  @ Thu, 19 May 2016 15:49:29:  8000000 
INFO  @ Thu, 19 May 2016 15:49:31:  9000000 
INFO  @ Thu, 19 May 2016 15:49:33:  10000000 
INFO  @ Thu, 19 May 2016 15:49:35:  11000000 
INFO  @ Thu, 19 May 2016 15:49:37:  12000000 
INFO  @ Thu, 19 May 2016 15:49:39:  13000000 
INFO  @ Thu, 19 May 2016 15:49:41:  14000000 
INFO  @ Thu, 19 May 2016 15:49:43:  15000000 
INFO  @ Thu, 19 May 2016 15:49:45:  16000000 
INFO  @ Thu, 19 May 2016 15:49:47:  17000000 
INFO  @ Thu, 19 May 2016 15:49:49:  18000000 
INFO  @ Thu, 19 May 2016 15:49:51:  19000000 
INFO  @ Thu, 19 May 2016 15:49:53:  20000000 
INFO  @ Thu, 19 May 2016 15:49:55:  21000000 
INFO  @ Thu, 19 May 2016 15:49:57:  22000000 
INFO  @ Thu, 19 May 2016 15:49:59:  23000000 
INFO  @ Thu, 19 May 2016 15:50:01:  24000000 
INFO  @ Thu, 19 May 2016 15:50:03:  25000000 
INFO  @ Thu, 19 May 2016 15:50:05:  26000000 
INFO  @ Thu, 19 May 2016 15:50:07:  27000000 
INFO  @ Thu, 19 May 2016 15:50:09:  28000000 
INFO  @ Thu, 19 May 2016 15:50:11:  29000000 
INFO  @ Thu, 19 May 2016 15:50:13:  30000000 
INFO  @ Thu, 19 May 2016 15:50:15:  31000000 
INFO  @ Thu, 19 May 2016 15:50:17:  32000000 
INFO  @ Thu, 19 May 2016 15:50:19:  33000000 
INFO  @ Thu, 19 May 2016 15:50:22:  34000000 
INFO  @ Thu, 19 May 2016 15:50:24:  35000000 
INFO  @ Thu, 19 May 2016 15:50:26:  36000000 
INFO  @ Thu, 19 May 2016 15:50:28:  37000000 
INFO  @ Thu, 19 May 2016 15:50:30:  38000000 
INFO  @ Thu, 19 May 2016 15:50:32:  39000000 
INFO  @ Thu, 19 May 2016 15:50:34:  40000000 
INFO  @ Thu, 19 May 2016 15:50:36:  41000000 
INFO  @ Thu, 19 May 2016 15:50:38:  42000000 
INFO  @ Thu, 19 May 2016 15:50:40:  43000000 
INFO  @ Thu, 19 May 2016 15:50:42:  44000000 
INFO  @ Thu, 19 May 2016 15:50:44:  45000000 
INFO  @ Thu, 19 May 2016 15:50:46:  46000000 
INFO  @ Thu, 19 May 2016 15:50:48:  47000000 
INFO  @ Thu, 19 May 2016 15:50:51:  48000000 
INFO  @ Thu, 19 May 2016 15:50:53:  49000000 
INFO  @ Thu, 19 May 2016 15:50:55:  50000000 
INFO  @ Thu, 19 May 2016 15:51:00: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 15:51:00: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 15:51:00: #1  total tags in treatment: 50529648 
INFO  @ Thu, 19 May 2016 15:51:00: #1 finished! 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:51:00: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:51:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 15:51:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 15:53:23: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 15:56:55: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 15:56:59: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 15:57:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 15:57:04: Done! 
INFO  @ Thu, 19 May 2016 15:57:18: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:57:18: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:57:18: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:57:20:  1000000 
INFO  @ Thu, 19 May 2016 15:57:23:  2000000 
INFO  @ Thu, 19 May 2016 15:57:25:  3000000 
INFO  @ Thu, 19 May 2016 15:57:27:  4000000 
INFO  @ Thu, 19 May 2016 15:57:29:  5000000 
INFO  @ Thu, 19 May 2016 15:57:31:  6000000 
INFO  @ Thu, 19 May 2016 15:57:33:  7000000 
INFO  @ Thu, 19 May 2016 15:57:35:  8000000 
INFO  @ Thu, 19 May 2016 15:57:38:  9000000 
INFO  @ Thu, 19 May 2016 15:57:40:  10000000 
INFO  @ Thu, 19 May 2016 15:57:42:  11000000 
INFO  @ Thu, 19 May 2016 15:57:44:  12000000 
INFO  @ Thu, 19 May 2016 15:57:46:  13000000 
INFO  @ Thu, 19 May 2016 15:57:48:  14000000 
INFO  @ Thu, 19 May 2016 15:57:50:  15000000 
INFO  @ Thu, 19 May 2016 15:57:52:  16000000 
INFO  @ Thu, 19 May 2016 15:57:54:  17000000 
INFO  @ Thu, 19 May 2016 15:57:57:  18000000 
INFO  @ Thu, 19 May 2016 15:57:59:  19000000 
INFO  @ Thu, 19 May 2016 15:58:01:  20000000 
INFO  @ Thu, 19 May 2016 15:58:03:  21000000 
INFO  @ Thu, 19 May 2016 15:58:05:  22000000 
INFO  @ Thu, 19 May 2016 15:58:07:  23000000 
INFO  @ Thu, 19 May 2016 15:58:09:  24000000 
INFO  @ Thu, 19 May 2016 15:58:12:  25000000 
INFO  @ Thu, 19 May 2016 15:58:14:  26000000 
INFO  @ Thu, 19 May 2016 15:58:16:  27000000 
INFO  @ Thu, 19 May 2016 15:58:18:  28000000 
INFO  @ Thu, 19 May 2016 15:58:20:  29000000 
INFO  @ Thu, 19 May 2016 15:58:22:  30000000 
INFO  @ Thu, 19 May 2016 15:58:25:  31000000 
INFO  @ Thu, 19 May 2016 15:58:27:  32000000 
INFO  @ Thu, 19 May 2016 15:58:29:  33000000 
INFO  @ Thu, 19 May 2016 15:58:31:  34000000 
INFO  @ Thu, 19 May 2016 15:58:33:  35000000 
INFO  @ Thu, 19 May 2016 15:58:35:  36000000 
INFO  @ Thu, 19 May 2016 15:58:37:  37000000 
INFO  @ Thu, 19 May 2016 15:58:39:  38000000 
INFO  @ Thu, 19 May 2016 15:58:41:  39000000 
INFO  @ Thu, 19 May 2016 15:58:43:  40000000 
INFO  @ Thu, 19 May 2016 15:58:45:  41000000 
INFO  @ Thu, 19 May 2016 15:58:48:  42000000 
INFO  @ Thu, 19 May 2016 15:58:50:  43000000 
INFO  @ Thu, 19 May 2016 15:58:52:  44000000 
INFO  @ Thu, 19 May 2016 15:58:54:  45000000 
INFO  @ Thu, 19 May 2016 15:58:56:  46000000 
INFO  @ Thu, 19 May 2016 15:58:58:  47000000 
INFO  @ Thu, 19 May 2016 15:59:01:  48000000 
INFO  @ Thu, 19 May 2016 15:59:03:  49000000 
INFO  @ Thu, 19 May 2016 15:59:05:  50000000 
INFO  @ Thu, 19 May 2016 15:59:10: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 15:59:10: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 15:59:10: #1  total tags in treatment: 50529648 
INFO  @ Thu, 19 May 2016 15:59:10: #1 finished! 
INFO  @ Thu, 19 May 2016 15:59:10: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:59:10: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:59:10: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:59:10: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:59:10: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:59:10: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 15:59:10: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 15:59:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 16:01:31: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 16:01:31: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 16:01:31: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 16:01:31: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 16:01:31: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 16:16:54: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 16:17:06: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 16:17:14: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 16:17:18: Done!

Num	17
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_22
Name	macs2_atac rep1
Thread	thread_20
PID	10070

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

Start	2016-05-19 15:49:05
End	2016-05-19 17:31:19
Elapsed	01:42:14
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.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:49:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:49:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:49:14:  1000000 
INFO  @ Thu, 19 May 2016 15:49:16:  2000000 
INFO  @ Thu, 19 May 2016 15:49:18:  3000000 
INFO  @ Thu, 19 May 2016 15:49:21:  4000000 
INFO  @ Thu, 19 May 2016 15:49:23:  5000000 
INFO  @ Thu, 19 May 2016 15:49:25:  6000000 
INFO  @ Thu, 19 May 2016 15:49:27:  7000000 
INFO  @ Thu, 19 May 2016 15:49:29:  8000000 
INFO  @ Thu, 19 May 2016 15:49:31:  9000000 
INFO  @ Thu, 19 May 2016 15:49:33:  10000000 
INFO  @ Thu, 19 May 2016 15:49:35:  11000000 
INFO  @ Thu, 19 May 2016 15:49:37:  12000000 
INFO  @ Thu, 19 May 2016 15:49:39:  13000000 
INFO  @ Thu, 19 May 2016 15:49:41:  14000000 
INFO  @ Thu, 19 May 2016 15:49:43:  15000000 
INFO  @ Thu, 19 May 2016 15:49:45:  16000000 
INFO  @ Thu, 19 May 2016 15:49:47:  17000000 
INFO  @ Thu, 19 May 2016 15:49:49:  18000000 
INFO  @ Thu, 19 May 2016 15:49:51:  19000000 
INFO  @ Thu, 19 May 2016 15:49:53:  20000000 
INFO  @ Thu, 19 May 2016 15:49:55:  21000000 
INFO  @ Thu, 19 May 2016 15:49:57:  22000000 
INFO  @ Thu, 19 May 2016 15:49:59:  23000000 
INFO  @ Thu, 19 May 2016 15:50:01:  24000000 
INFO  @ Thu, 19 May 2016 15:50:03:  25000000 
INFO  @ Thu, 19 May 2016 15:50:05:  26000000 
INFO  @ Thu, 19 May 2016 15:50:07:  27000000 
INFO  @ Thu, 19 May 2016 15:50:09:  28000000 
INFO  @ Thu, 19 May 2016 15:50:11:  29000000 
INFO  @ Thu, 19 May 2016 15:50:13:  30000000 
INFO  @ Thu, 19 May 2016 15:50:15:  31000000 
INFO  @ Thu, 19 May 2016 15:50:17:  32000000 
INFO  @ Thu, 19 May 2016 15:50:19:  33000000 
INFO  @ Thu, 19 May 2016 15:50:21:  34000000 
INFO  @ Thu, 19 May 2016 15:50:23:  35000000 
INFO  @ Thu, 19 May 2016 15:50:25:  36000000 
INFO  @ Thu, 19 May 2016 15:50:28:  37000000 
INFO  @ Thu, 19 May 2016 15:50:30:  38000000 
INFO  @ Thu, 19 May 2016 15:50:32:  39000000 
INFO  @ Thu, 19 May 2016 15:50:34:  40000000 
INFO  @ Thu, 19 May 2016 15:50:36:  41000000 
INFO  @ Thu, 19 May 2016 15:50:38:  42000000 
INFO  @ Thu, 19 May 2016 15:50:40:  43000000 
INFO  @ Thu, 19 May 2016 15:50:43:  44000000 
INFO  @ Thu, 19 May 2016 15:50:45:  45000000 
INFO  @ Thu, 19 May 2016 15:50:47:  46000000 
INFO  @ Thu, 19 May 2016 15:50:49:  47000000 
INFO  @ Thu, 19 May 2016 15:50:51:  48000000 
INFO  @ Thu, 19 May 2016 15:50:53:  49000000 
INFO  @ Thu, 19 May 2016 15:50:55:  50000000 
INFO  @ Thu, 19 May 2016 15:51:00: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 15:51:00: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 15:51:00: #1  total tags in treatment: 50529648 
INFO  @ Thu, 19 May 2016 15:51:00: #1 finished! 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:51:00: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:51:00: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:51:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 15:51:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 15:53:20: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 15:56:32: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Thu, 19 May 2016 15:56:36: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 15:56:39: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 15:56:41: Done! 
INFO  @ Thu, 19 May 2016 15:56:57: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 15:56:57: #1 read tag files... 
INFO  @ Thu, 19 May 2016 15:56:57: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 15:56:59:  1000000 
INFO  @ Thu, 19 May 2016 15:57:01:  2000000 
INFO  @ Thu, 19 May 2016 15:57:04:  3000000 
INFO  @ Thu, 19 May 2016 15:57:06:  4000000 
INFO  @ Thu, 19 May 2016 15:57:09:  5000000 
INFO  @ Thu, 19 May 2016 15:57:11:  6000000 
INFO  @ Thu, 19 May 2016 15:57:14:  7000000 
INFO  @ Thu, 19 May 2016 15:57:16:  8000000 
INFO  @ Thu, 19 May 2016 15:57:19:  9000000 
INFO  @ Thu, 19 May 2016 15:57:21:  10000000 
INFO  @ Thu, 19 May 2016 15:57:24:  11000000 
INFO  @ Thu, 19 May 2016 15:57:26:  12000000 
INFO  @ Thu, 19 May 2016 15:57:29:  13000000 
INFO  @ Thu, 19 May 2016 15:57:31:  14000000 
INFO  @ Thu, 19 May 2016 15:57:33:  15000000 
INFO  @ Thu, 19 May 2016 15:57:36:  16000000 
INFO  @ Thu, 19 May 2016 15:57:39:  17000000 
INFO  @ Thu, 19 May 2016 15:57:41:  18000000 
INFO  @ Thu, 19 May 2016 15:57:43:  19000000 
INFO  @ Thu, 19 May 2016 15:57:46:  20000000 
INFO  @ Thu, 19 May 2016 15:57:48:  21000000 
INFO  @ Thu, 19 May 2016 15:57:51:  22000000 
INFO  @ Thu, 19 May 2016 15:57:53:  23000000 
INFO  @ Thu, 19 May 2016 15:57:56:  24000000 
INFO  @ Thu, 19 May 2016 15:57:58:  25000000 
INFO  @ Thu, 19 May 2016 15:58:01:  26000000 
INFO  @ Thu, 19 May 2016 15:58:03:  27000000 
INFO  @ Thu, 19 May 2016 15:58:06:  28000000 
INFO  @ Thu, 19 May 2016 15:58:08:  29000000 
INFO  @ Thu, 19 May 2016 15:58:11:  30000000 
INFO  @ Thu, 19 May 2016 15:58:14:  31000000 
INFO  @ Thu, 19 May 2016 15:58:16:  32000000 
INFO  @ Thu, 19 May 2016 15:58:19:  33000000 
INFO  @ Thu, 19 May 2016 15:58:21:  34000000 
INFO  @ Thu, 19 May 2016 15:58:23:  35000000 
INFO  @ Thu, 19 May 2016 15:58:26:  36000000 
INFO  @ Thu, 19 May 2016 15:58:29:  37000000 
INFO  @ Thu, 19 May 2016 15:58:31:  38000000 
INFO  @ Thu, 19 May 2016 15:58:33:  39000000 
INFO  @ Thu, 19 May 2016 15:58:36:  40000000 
INFO  @ Thu, 19 May 2016 15:58:39:  41000000 
INFO  @ Thu, 19 May 2016 15:58:41:  42000000 
INFO  @ Thu, 19 May 2016 15:58:43:  43000000 
INFO  @ Thu, 19 May 2016 15:58:46:  44000000 
INFO  @ Thu, 19 May 2016 15:58:48:  45000000 
INFO  @ Thu, 19 May 2016 15:58:51:  46000000 
INFO  @ Thu, 19 May 2016 15:58:53:  47000000 
INFO  @ Thu, 19 May 2016 15:58:56:  48000000 
INFO  @ Thu, 19 May 2016 15:58:58:  49000000 
INFO  @ Thu, 19 May 2016 15:59:01:  50000000 
INFO  @ Thu, 19 May 2016 15:59:07: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 15:59:07: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 15:59:07: #1  total tags in treatment: 50529648 
INFO  @ Thu, 19 May 2016 15:59:07: #1 finished! 
INFO  @ Thu, 19 May 2016 15:59:07: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 15:59:07: #2 Skipped... 
INFO  @ Thu, 19 May 2016 15:59:07: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 15:59:07: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 15:59:07: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 15:59:07: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 15:59:07: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 19 May 2016 15:59:07: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 16:02:18: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 16:02:18: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 16:02:18: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 16:02:18: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 16:02:18: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 16:16:14: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Thu, 19 May 2016 16:16:20: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 16:16:25: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Thu, 19 May 2016 16:16:28: Done! 
INFO  @ Thu, 19 May 2016 16:16:48: Read and build treatment bedGraph... 
INFO  @ Thu, 19 May 2016 16:20:05: Read and build control bedGraph... 
INFO  @ Thu, 19 May 2016 16:21:12: Build scoreTrackII... 
INFO  @ Thu, 19 May 2016 16:22:56: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 19 May 2016 16:35:17: Write bedGraph of scores... 
INFO  @ Thu, 19 May 2016 16:42:05: Finished 'FE'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
INFO  @ Thu, 19 May 2016 16:56:35: Read and build treatment bedGraph... 
INFO  @ Thu, 19 May 2016 16:58:56: Read and build control bedGraph... 
INFO  @ Thu, 19 May 2016 16:59:43: Build scoreTrackII... 
INFO  @ Thu, 19 May 2016 17:00:43: Values in your input bedGraph files will be multiplied by 50.529648 ... 
INFO  @ Thu, 19 May 2016 17:07:35: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 19 May 2016 17:09:04: Write bedGraph of scores... 
INFO  @ Thu, 19 May 2016 17:14:47: Finished 'ppois'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	17978

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

Start	2016-05-19 18:26:47
End	2016-05-19 18:48:18
Elapsed	00:21:31
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.PE2SE.nodup.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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 19 files...

Num	19
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_24
Name	bam_to_bedpe rep2
Thread	thread_21
PID	24456

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

Start	2016-05-19 18:48:19
End	2016-05-19 18:50:44
Elapsed	00:02:25
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.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	26148

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

Start	2016-05-19 18:50:45
End	2016-05-19 18:53:12
Elapsed	00:02:26
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.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	26231

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

Start	2016-05-19 18:53:13
End	2016-05-19 18:56:19
Elapsed	00:03:06
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.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.00" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.01" | \
			gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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	27880

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

Start	2016-05-19 18:56:20
End	2016-05-19 18:57:39
Elapsed	00:01:19
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.PE2SE.nodup.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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	27885

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

Start	2016-05-19 18:56:20
End	2016-05-19 18:57:05
Elapsed	00:00:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	27893

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

Start	2016-05-19 18:56:20
End	2016-05-19 18:57:04
Elapsed	00:00:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	28101

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

Start	2016-05-19 18:57:40
End	2016-05-19 19:00:05
Elapsed	00:02:24
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.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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	28442

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

Start	2016-05-19 19:00:06
End	2016-05-19 19:31:41
Elapsed	00:31:35
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.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpknTb2u/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign70d64c658dab
done. read 20265285 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1243443 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.229495878625701 
Top 3 estimates for fragment length 0 
Window half size 490 
Phantom peak location 80 
Phantom peak Correlation 0.2504911 
Normalized Strand cross-correlation coefficient (NSC) 1.845648 
Relative Strand Cross correlation Coefficient (RSC) 0.8335649 
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	28444

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

Start	2016-05-19 19:00:06
End	2016-05-19 19:12:41
Elapsed	00:12:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:00:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:00:14:  1000000 
INFO  @ Thu, 19 May 2016 19:00:16:  2000000 
INFO  @ Thu, 19 May 2016 19:00:18:  3000000 
INFO  @ Thu, 19 May 2016 19:00:20:  4000000 
INFO  @ Thu, 19 May 2016 19:00:22:  5000000 
INFO  @ Thu, 19 May 2016 19:00:24:  6000000 
INFO  @ Thu, 19 May 2016 19:00:26:  7000000 
INFO  @ Thu, 19 May 2016 19:00:28:  8000000 
INFO  @ Thu, 19 May 2016 19:00:30:  9000000 
INFO  @ Thu, 19 May 2016 19:00:32:  10000000 
INFO  @ Thu, 19 May 2016 19:00:34:  11000000 
INFO  @ Thu, 19 May 2016 19:00:36:  12000000 
INFO  @ Thu, 19 May 2016 19:00:38:  13000000 
INFO  @ Thu, 19 May 2016 19:00:40:  14000000 
INFO  @ Thu, 19 May 2016 19:00:42:  15000000 
INFO  @ Thu, 19 May 2016 19:00:44:  16000000 
INFO  @ Thu, 19 May 2016 19:00:46:  17000000 
INFO  @ Thu, 19 May 2016 19:00:48:  18000000 
INFO  @ Thu, 19 May 2016 19:00:50:  19000000 
INFO  @ Thu, 19 May 2016 19:00:52:  20000000 
INFO  @ Thu, 19 May 2016 19:00:54:  21000000 
INFO  @ Thu, 19 May 2016 19:00:56:  22000000 
INFO  @ Thu, 19 May 2016 19:00:59: #1 tag size is determined as 69 bps 
INFO  @ Thu, 19 May 2016 19:00:59: #1 tag size = 69 
INFO  @ Thu, 19 May 2016 19:00:59: #1  total tags in treatment: 22474658 
INFO  @ Thu, 19 May 2016 19:00:59: #1 finished! 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:00:59: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:00:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:00:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:02:19: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:04:01: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 19:04:04: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 19:04:06: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 19:04:08: Done! 
INFO  @ Thu, 19 May 2016 19:04:27: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:04:27: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:04:27: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:04:29:  1000000 
INFO  @ Thu, 19 May 2016 19:04:31:  2000000 
INFO  @ Thu, 19 May 2016 19:04:33:  3000000 
INFO  @ Thu, 19 May 2016 19:04:35:  4000000 
INFO  @ Thu, 19 May 2016 19:04:37:  5000000 
INFO  @ Thu, 19 May 2016 19:04:39:  6000000 
INFO  @ Thu, 19 May 2016 19:04:41:  7000000 
INFO  @ Thu, 19 May 2016 19:04:43:  8000000 
INFO  @ Thu, 19 May 2016 19:04:45:  9000000 
INFO  @ Thu, 19 May 2016 19:04:47:  10000000 
INFO  @ Thu, 19 May 2016 19:04:49:  11000000 
INFO  @ Thu, 19 May 2016 19:04:51:  12000000 
INFO  @ Thu, 19 May 2016 19:04:53:  13000000 
INFO  @ Thu, 19 May 2016 19:04:55:  14000000 
INFO  @ Thu, 19 May 2016 19:04:57:  15000000 
INFO  @ Thu, 19 May 2016 19:04:59:  16000000 
INFO  @ Thu, 19 May 2016 19:05:01:  17000000 
INFO  @ Thu, 19 May 2016 19:05:03:  18000000 
INFO  @ Thu, 19 May 2016 19:05:05:  19000000 
INFO  @ Thu, 19 May 2016 19:05:07:  20000000 
INFO  @ Thu, 19 May 2016 19:05:09:  21000000 
INFO  @ Thu, 19 May 2016 19:05:11:  22000000 
INFO  @ Thu, 19 May 2016 19:05:14: #1 tag size is determined as 69 bps 
INFO  @ Thu, 19 May 2016 19:05:14: #1 tag size = 69 
INFO  @ Thu, 19 May 2016 19:05:14: #1  total tags in treatment: 22474658 
INFO  @ Thu, 19 May 2016 19:05:14: #1 finished! 
INFO  @ Thu, 19 May 2016 19:05:14: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:05:14: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:05:14: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:05:14: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:05:14: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:05:14: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 19:05:14: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 19:05:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:06:36: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 19:06:36: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 19:06:36: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 19:06:36: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 19:06:36: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:12:24: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 19:12:28: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 19:12:31: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 19:12:33: 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	28454

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

Start	2016-05-19 19:00:06
End	2016-05-19 19:12:27
Elapsed	00:12:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:00:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:00:14:  1000000 
INFO  @ Thu, 19 May 2016 19:00:16:  2000000 
INFO  @ Thu, 19 May 2016 19:00:18:  3000000 
INFO  @ Thu, 19 May 2016 19:00:20:  4000000 
INFO  @ Thu, 19 May 2016 19:00:22:  5000000 
INFO  @ Thu, 19 May 2016 19:00:24:  6000000 
INFO  @ Thu, 19 May 2016 19:00:26:  7000000 
INFO  @ Thu, 19 May 2016 19:00:28:  8000000 
INFO  @ Thu, 19 May 2016 19:00:30:  9000000 
INFO  @ Thu, 19 May 2016 19:00:32:  10000000 
INFO  @ Thu, 19 May 2016 19:00:34:  11000000 
INFO  @ Thu, 19 May 2016 19:00:36:  12000000 
INFO  @ Thu, 19 May 2016 19:00:38:  13000000 
INFO  @ Thu, 19 May 2016 19:00:40:  14000000 
INFO  @ Thu, 19 May 2016 19:00:42:  15000000 
INFO  @ Thu, 19 May 2016 19:00:44:  16000000 
INFO  @ Thu, 19 May 2016 19:00:46:  17000000 
INFO  @ Thu, 19 May 2016 19:00:48:  18000000 
INFO  @ Thu, 19 May 2016 19:00:50:  19000000 
INFO  @ Thu, 19 May 2016 19:00:52:  20000000 
INFO  @ Thu, 19 May 2016 19:00:54:  21000000 
INFO  @ Thu, 19 May 2016 19:00:56:  22000000 
INFO  @ Thu, 19 May 2016 19:00:59: #1 tag size is determined as 52 bps 
INFO  @ Thu, 19 May 2016 19:00:59: #1 tag size = 52 
INFO  @ Thu, 19 May 2016 19:00:59: #1  total tags in treatment: 22474658 
INFO  @ Thu, 19 May 2016 19:00:59: #1 finished! 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:00:59: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:00:59: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:00:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:00:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:02:18: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:04:01: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 19:04:04: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 19:04:06: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 19:04:08: Done! 
INFO  @ Thu, 19 May 2016 19:04:23: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:04:23: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:04:23: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:04:25:  1000000 
INFO  @ Thu, 19 May 2016 19:04:27:  2000000 
INFO  @ Thu, 19 May 2016 19:04:29:  3000000 
INFO  @ Thu, 19 May 2016 19:04:31:  4000000 
INFO  @ Thu, 19 May 2016 19:04:33:  5000000 
INFO  @ Thu, 19 May 2016 19:04:35:  6000000 
INFO  @ Thu, 19 May 2016 19:04:37:  7000000 
INFO  @ Thu, 19 May 2016 19:04:39:  8000000 
INFO  @ Thu, 19 May 2016 19:04:41:  9000000 
INFO  @ Thu, 19 May 2016 19:04:43:  10000000 
INFO  @ Thu, 19 May 2016 19:04:45:  11000000 
INFO  @ Thu, 19 May 2016 19:04:47:  12000000 
INFO  @ Thu, 19 May 2016 19:04:49:  13000000 
INFO  @ Thu, 19 May 2016 19:04:51:  14000000 
INFO  @ Thu, 19 May 2016 19:04:53:  15000000 
INFO  @ Thu, 19 May 2016 19:04:55:  16000000 
INFO  @ Thu, 19 May 2016 19:04:57:  17000000 
INFO  @ Thu, 19 May 2016 19:04:59:  18000000 
INFO  @ Thu, 19 May 2016 19:05:01:  19000000 
INFO  @ Thu, 19 May 2016 19:05:03:  20000000 
INFO  @ Thu, 19 May 2016 19:05:05:  21000000 
INFO  @ Thu, 19 May 2016 19:05:07:  22000000 
INFO  @ Thu, 19 May 2016 19:05:10: #1 tag size is determined as 52 bps 
INFO  @ Thu, 19 May 2016 19:05:10: #1 tag size = 52 
INFO  @ Thu, 19 May 2016 19:05:10: #1  total tags in treatment: 22474658 
INFO  @ Thu, 19 May 2016 19:05:10: #1 finished! 
INFO  @ Thu, 19 May 2016 19:05:10: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:05:10: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:05:10: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:05:10: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:05:10: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:05:10: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 19:05:10: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 19:05:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:06:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 19:06:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 19:06:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 19:06:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 19:06:33: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:12:10: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 19:12:14: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 19:12:17: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 19:12:19: 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	28468

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

Start	2016-05-19 19:00:06
End	2016-05-19 19:19:20
Elapsed	00:19:14
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.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:00:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:00:14:  1000000 
INFO  @ Thu, 19 May 2016 19:00:16:  2000000 
INFO  @ Thu, 19 May 2016 19:00:18:  3000000 
INFO  @ Thu, 19 May 2016 19:00:20:  4000000 
INFO  @ Thu, 19 May 2016 19:00:22:  5000000 
INFO  @ Thu, 19 May 2016 19:00:24:  6000000 
INFO  @ Thu, 19 May 2016 19:00:26:  7000000 
INFO  @ Thu, 19 May 2016 19:00:28:  8000000 
INFO  @ Thu, 19 May 2016 19:00:30:  9000000 
INFO  @ Thu, 19 May 2016 19:00:32:  10000000 
INFO  @ Thu, 19 May 2016 19:00:34:  11000000 
INFO  @ Thu, 19 May 2016 19:00:36:  12000000 
INFO  @ Thu, 19 May 2016 19:00:38:  13000000 
INFO  @ Thu, 19 May 2016 19:00:40:  14000000 
INFO  @ Thu, 19 May 2016 19:00:42:  15000000 
INFO  @ Thu, 19 May 2016 19:00:44:  16000000 
INFO  @ Thu, 19 May 2016 19:00:46:  17000000 
INFO  @ Thu, 19 May 2016 19:00:48:  18000000 
INFO  @ Thu, 19 May 2016 19:00:50:  19000000 
INFO  @ Thu, 19 May 2016 19:00:52:  20000000 
INFO  @ Thu, 19 May 2016 19:00:54:  21000000 
INFO  @ Thu, 19 May 2016 19:00:56:  22000000 
INFO  @ Thu, 19 May 2016 19:00:58:  23000000 
INFO  @ Thu, 19 May 2016 19:01:00:  24000000 
INFO  @ Thu, 19 May 2016 19:01:02:  25000000 
INFO  @ Thu, 19 May 2016 19:01:05:  26000000 
INFO  @ Thu, 19 May 2016 19:01:07:  27000000 
INFO  @ Thu, 19 May 2016 19:01:09:  28000000 
INFO  @ Thu, 19 May 2016 19:01:11:  29000000 
INFO  @ Thu, 19 May 2016 19:01:13:  30000000 
INFO  @ Thu, 19 May 2016 19:01:15:  31000000 
INFO  @ Thu, 19 May 2016 19:01:17:  32000000 
INFO  @ Thu, 19 May 2016 19:01:19:  33000000 
INFO  @ Thu, 19 May 2016 19:01:21:  34000000 
INFO  @ Thu, 19 May 2016 19:01:23:  35000000 
INFO  @ Thu, 19 May 2016 19:01:25:  36000000 
INFO  @ Thu, 19 May 2016 19:01:27:  37000000 
INFO  @ Thu, 19 May 2016 19:01:29:  38000000 
INFO  @ Thu, 19 May 2016 19:01:31:  39000000 
INFO  @ Thu, 19 May 2016 19:01:33:  40000000 
INFO  @ Thu, 19 May 2016 19:01:38: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 19:01:38: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 19:01:38: #1  total tags in treatment: 40530570 
INFO  @ Thu, 19 May 2016 19:01:38: #1 finished! 
INFO  @ Thu, 19 May 2016 19:01:38: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:01:38: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:01:38: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:01:38: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:01:38: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:01:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:01:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:03:41: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:06:42: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 19:06:45: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 19:06:48: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 19:06:50: Done! 
INFO  @ Thu, 19 May 2016 19:07:11: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:07:11: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:07:11: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:07:13:  1000000 
INFO  @ Thu, 19 May 2016 19:07:16:  2000000 
INFO  @ Thu, 19 May 2016 19:07:18:  3000000 
INFO  @ Thu, 19 May 2016 19:07:20:  4000000 
INFO  @ Thu, 19 May 2016 19:07:22:  5000000 
INFO  @ Thu, 19 May 2016 19:07:24:  6000000 
INFO  @ Thu, 19 May 2016 19:07:26:  7000000 
INFO  @ Thu, 19 May 2016 19:07:28:  8000000 
INFO  @ Thu, 19 May 2016 19:07:30:  9000000 
INFO  @ Thu, 19 May 2016 19:07:32:  10000000 
INFO  @ Thu, 19 May 2016 19:07:34:  11000000 
INFO  @ Thu, 19 May 2016 19:07:36:  12000000 
INFO  @ Thu, 19 May 2016 19:07:38:  13000000 
INFO  @ Thu, 19 May 2016 19:07:40:  14000000 
INFO  @ Thu, 19 May 2016 19:07:42:  15000000 
INFO  @ Thu, 19 May 2016 19:07:44:  16000000 
INFO  @ Thu, 19 May 2016 19:07:46:  17000000 
INFO  @ Thu, 19 May 2016 19:07:48:  18000000 
INFO  @ Thu, 19 May 2016 19:07:51:  19000000 
INFO  @ Thu, 19 May 2016 19:07:53:  20000000 
INFO  @ Thu, 19 May 2016 19:07:55:  21000000 
INFO  @ Thu, 19 May 2016 19:07:57:  22000000 
INFO  @ Thu, 19 May 2016 19:07:59:  23000000 
INFO  @ Thu, 19 May 2016 19:08:01:  24000000 
INFO  @ Thu, 19 May 2016 19:08:03:  25000000 
INFO  @ Thu, 19 May 2016 19:08:05:  26000000 
INFO  @ Thu, 19 May 2016 19:08:07:  27000000 
INFO  @ Thu, 19 May 2016 19:08:09:  28000000 
INFO  @ Thu, 19 May 2016 19:08:11:  29000000 
INFO  @ Thu, 19 May 2016 19:08:14:  30000000 
INFO  @ Thu, 19 May 2016 19:08:16:  31000000 
INFO  @ Thu, 19 May 2016 19:08:18:  32000000 
INFO  @ Thu, 19 May 2016 19:08:20:  33000000 
INFO  @ Thu, 19 May 2016 19:08:22:  34000000 
INFO  @ Thu, 19 May 2016 19:08:24:  35000000 
INFO  @ Thu, 19 May 2016 19:08:26:  36000000 
INFO  @ Thu, 19 May 2016 19:08:28:  37000000 
INFO  @ Thu, 19 May 2016 19:08:30:  38000000 
INFO  @ Thu, 19 May 2016 19:08:32:  39000000 
INFO  @ Thu, 19 May 2016 19:08:34:  40000000 
INFO  @ Thu, 19 May 2016 19:08:39: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 19:08:39: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 19:08:39: #1  total tags in treatment: 40530570 
INFO  @ Thu, 19 May 2016 19:08:39: #1 finished! 
INFO  @ Thu, 19 May 2016 19:08:39: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:08:39: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:08:39: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:08:39: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:08:39: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:08:39: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 19:08:39: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 19:08:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:10:51: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 19:10:51: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 19:10:51: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 19:10:51: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 19:10:51: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:19:01: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 19:19:06: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 19:19:10: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 19:19:12: Done!

Num	30
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_35
Name	macs2_atac rep2
Thread	thread_21
PID	28495

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

Start	2016-05-19 19:00:06
End	2016-05-19 19:50:29
Elapsed	00:50:22
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.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:00:12: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:00:12: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:00:14:  1000000 
INFO  @ Thu, 19 May 2016 19:00:16:  2000000 
INFO  @ Thu, 19 May 2016 19:00:18:  3000000 
INFO  @ Thu, 19 May 2016 19:00:20:  4000000 
INFO  @ Thu, 19 May 2016 19:00:22:  5000000 
INFO  @ Thu, 19 May 2016 19:00:24:  6000000 
INFO  @ Thu, 19 May 2016 19:00:26:  7000000 
INFO  @ Thu, 19 May 2016 19:00:28:  8000000 
INFO  @ Thu, 19 May 2016 19:00:30:  9000000 
INFO  @ Thu, 19 May 2016 19:00:32:  10000000 
INFO  @ Thu, 19 May 2016 19:00:34:  11000000 
INFO  @ Thu, 19 May 2016 19:00:36:  12000000 
INFO  @ Thu, 19 May 2016 19:00:38:  13000000 
INFO  @ Thu, 19 May 2016 19:00:40:  14000000 
INFO  @ Thu, 19 May 2016 19:00:42:  15000000 
INFO  @ Thu, 19 May 2016 19:00:45:  16000000 
INFO  @ Thu, 19 May 2016 19:00:47:  17000000 
INFO  @ Thu, 19 May 2016 19:00:49:  18000000 
INFO  @ Thu, 19 May 2016 19:00:51:  19000000 
INFO  @ Thu, 19 May 2016 19:00:53:  20000000 
INFO  @ Thu, 19 May 2016 19:00:55:  21000000 
INFO  @ Thu, 19 May 2016 19:00:57:  22000000 
INFO  @ Thu, 19 May 2016 19:00:59:  23000000 
INFO  @ Thu, 19 May 2016 19:01:01:  24000000 
INFO  @ Thu, 19 May 2016 19:01:03:  25000000 
INFO  @ Thu, 19 May 2016 19:01:05:  26000000 
INFO  @ Thu, 19 May 2016 19:01:07:  27000000 
INFO  @ Thu, 19 May 2016 19:01:09:  28000000 
INFO  @ Thu, 19 May 2016 19:01:12:  29000000 
INFO  @ Thu, 19 May 2016 19:01:14:  30000000 
INFO  @ Thu, 19 May 2016 19:01:16:  31000000 
INFO  @ Thu, 19 May 2016 19:01:18:  32000000 
INFO  @ Thu, 19 May 2016 19:01:20:  33000000 
INFO  @ Thu, 19 May 2016 19:01:22:  34000000 
INFO  @ Thu, 19 May 2016 19:01:24:  35000000 
INFO  @ Thu, 19 May 2016 19:01:26:  36000000 
INFO  @ Thu, 19 May 2016 19:01:28:  37000000 
INFO  @ Thu, 19 May 2016 19:01:30:  38000000 
INFO  @ Thu, 19 May 2016 19:01:32:  39000000 
INFO  @ Thu, 19 May 2016 19:01:34:  40000000 
INFO  @ Thu, 19 May 2016 19:01:39: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 19:01:39: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 19:01:39: #1  total tags in treatment: 40530570 
INFO  @ Thu, 19 May 2016 19:01:39: #1 finished! 
INFO  @ Thu, 19 May 2016 19:01:39: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:01:39: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:01:39: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:01:39: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:01:39: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:01:39: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:01:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:03:49: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:06:33: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Thu, 19 May 2016 19:06:36: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 19:06:38: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 19:06:41: Done! 
INFO  @ Thu, 19 May 2016 19:07:07: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:07:07: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:07:07: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:07:09:  1000000 
INFO  @ Thu, 19 May 2016 19:07:11:  2000000 
INFO  @ Thu, 19 May 2016 19:07:13:  3000000 
INFO  @ Thu, 19 May 2016 19:07:15:  4000000 
INFO  @ Thu, 19 May 2016 19:07:17:  5000000 
INFO  @ Thu, 19 May 2016 19:07:19:  6000000 
INFO  @ Thu, 19 May 2016 19:07:21:  7000000 
INFO  @ Thu, 19 May 2016 19:07:23:  8000000 
INFO  @ Thu, 19 May 2016 19:07:25:  9000000 
INFO  @ Thu, 19 May 2016 19:07:27:  10000000 
INFO  @ Thu, 19 May 2016 19:07:29:  11000000 
INFO  @ Thu, 19 May 2016 19:07:31:  12000000 
INFO  @ Thu, 19 May 2016 19:07:33:  13000000 
INFO  @ Thu, 19 May 2016 19:07:35:  14000000 
INFO  @ Thu, 19 May 2016 19:07:37:  15000000 
INFO  @ Thu, 19 May 2016 19:07:39:  16000000 
INFO  @ Thu, 19 May 2016 19:07:41:  17000000 
INFO  @ Thu, 19 May 2016 19:07:43:  18000000 
INFO  @ Thu, 19 May 2016 19:07:45:  19000000 
INFO  @ Thu, 19 May 2016 19:07:47:  20000000 
INFO  @ Thu, 19 May 2016 19:07:49:  21000000 
INFO  @ Thu, 19 May 2016 19:07:51:  22000000 
INFO  @ Thu, 19 May 2016 19:07:53:  23000000 
INFO  @ Thu, 19 May 2016 19:07:55:  24000000 
INFO  @ Thu, 19 May 2016 19:07:57:  25000000 
INFO  @ Thu, 19 May 2016 19:07:59:  26000000 
INFO  @ Thu, 19 May 2016 19:08:01:  27000000 
INFO  @ Thu, 19 May 2016 19:08:03:  28000000 
INFO  @ Thu, 19 May 2016 19:08:05:  29000000 
INFO  @ Thu, 19 May 2016 19:08:07:  30000000 
INFO  @ Thu, 19 May 2016 19:08:09:  31000000 
INFO  @ Thu, 19 May 2016 19:08:11:  32000000 
INFO  @ Thu, 19 May 2016 19:08:13:  33000000 
INFO  @ Thu, 19 May 2016 19:08:15:  34000000 
INFO  @ Thu, 19 May 2016 19:08:17:  35000000 
INFO  @ Thu, 19 May 2016 19:08:19:  36000000 
INFO  @ Thu, 19 May 2016 19:08:22:  37000000 
INFO  @ Thu, 19 May 2016 19:08:24:  38000000 
INFO  @ Thu, 19 May 2016 19:08:26:  39000000 
INFO  @ Thu, 19 May 2016 19:08:28:  40000000 
INFO  @ Thu, 19 May 2016 19:08:32: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 19:08:32: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 19:08:32: #1  total tags in treatment: 40530570 
INFO  @ Thu, 19 May 2016 19:08:32: #1 finished! 
INFO  @ Thu, 19 May 2016 19:08:32: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:08:32: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:08:32: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:08:32: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:08:32: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:08:32: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 19:08:32: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 19 May 2016 19:08:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:10:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 19:10:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 19:10:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 19:10:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 19:10:33: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:17:02: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Thu, 19 May 2016 19:17:05: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 19:17:07: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Thu, 19 May 2016 19:17:08: Done! 
INFO  @ Thu, 19 May 2016 19:17:16: Read and build treatment bedGraph... 
INFO  @ Thu, 19 May 2016 19:18:42: Read and build control bedGraph... 
INFO  @ Thu, 19 May 2016 19:19:16: Build scoreTrackII... 
INFO  @ Thu, 19 May 2016 19:20:08: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 19 May 2016 19:24:27: Write bedGraph of scores... 
INFO  @ Thu, 19 May 2016 19:26:53: Finished 'FE'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
INFO  @ Thu, 19 May 2016 19:35:26: Read and build treatment bedGraph... 
INFO  @ Thu, 19 May 2016 19:36:50: Read and build control bedGraph... 
INFO  @ Thu, 19 May 2016 19:37:21: Build scoreTrackII... 
INFO  @ Thu, 19 May 2016 19:37:51: Values in your input bedGraph files will be multiplied by 40.530570 ... 
INFO  @ Thu, 19 May 2016 19:41:36: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 19 May 2016 19:42:13: Write bedGraph of scores... 
INFO  @ Thu, 19 May 2016 19:44:12: Finished 'ppois'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	46049

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

Start	2016-05-19 19:50:29
End	2016-05-19 19:53:01
Elapsed	00:02:32
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.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz  | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	46052

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

Start	2016-05-19 19:50:30
End	2016-05-19 19:51:57
Elapsed	00:01:27
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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	46061

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

Start	2016-05-19 19:50:30
End	2016-05-19 19:51:53
Elapsed	00:01:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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	46457

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

Start	2016-05-19 19:53:02
End	2016-05-19 20:23:01
Elapsed	00:29:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:53:05: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:53:07:  1000000 
INFO  @ Thu, 19 May 2016 19:53:09:  2000000 
INFO  @ Thu, 19 May 2016 19:53:11:  3000000 
INFO  @ Thu, 19 May 2016 19:53:14:  4000000 
INFO  @ Thu, 19 May 2016 19:53:16:  5000000 
INFO  @ Thu, 19 May 2016 19:53:18:  6000000 
INFO  @ Thu, 19 May 2016 19:53:20:  7000000 
INFO  @ Thu, 19 May 2016 19:53:22:  8000000 
INFO  @ Thu, 19 May 2016 19:53:24:  9000000 
INFO  @ Thu, 19 May 2016 19:53:26:  10000000 
INFO  @ Thu, 19 May 2016 19:53:28:  11000000 
INFO  @ Thu, 19 May 2016 19:53:30:  12000000 
INFO  @ Thu, 19 May 2016 19:53:33:  13000000 
INFO  @ Thu, 19 May 2016 19:53:35:  14000000 
INFO  @ Thu, 19 May 2016 19:53:37:  15000000 
INFO  @ Thu, 19 May 2016 19:53:39:  16000000 
INFO  @ Thu, 19 May 2016 19:53:41:  17000000 
INFO  @ Thu, 19 May 2016 19:53:43:  18000000 
INFO  @ Thu, 19 May 2016 19:53:45:  19000000 
INFO  @ Thu, 19 May 2016 19:53:47:  20000000 
INFO  @ Thu, 19 May 2016 19:53:50:  21000000 
INFO  @ Thu, 19 May 2016 19:53:52:  22000000 
INFO  @ Thu, 19 May 2016 19:53:54:  23000000 
INFO  @ Thu, 19 May 2016 19:53:56:  24000000 
INFO  @ Thu, 19 May 2016 19:53:58:  25000000 
INFO  @ Thu, 19 May 2016 19:54:00:  26000000 
INFO  @ Thu, 19 May 2016 19:54:02:  27000000 
INFO  @ Thu, 19 May 2016 19:54:04:  28000000 
INFO  @ Thu, 19 May 2016 19:54:07:  29000000 
INFO  @ Thu, 19 May 2016 19:54:09:  30000000 
INFO  @ Thu, 19 May 2016 19:54:11:  31000000 
INFO  @ Thu, 19 May 2016 19:54:13:  32000000 
INFO  @ Thu, 19 May 2016 19:54:15:  33000000 
INFO  @ Thu, 19 May 2016 19:54:17:  34000000 
INFO  @ Thu, 19 May 2016 19:54:19:  35000000 
INFO  @ Thu, 19 May 2016 19:54:21:  36000000 
INFO  @ Thu, 19 May 2016 19:54:24:  37000000 
INFO  @ Thu, 19 May 2016 19:54:26:  38000000 
INFO  @ Thu, 19 May 2016 19:54:28:  39000000 
INFO  @ Thu, 19 May 2016 19:54:30:  40000000 
INFO  @ Thu, 19 May 2016 19:54:32:  41000000 
INFO  @ Thu, 19 May 2016 19:54:34:  42000000 
INFO  @ Thu, 19 May 2016 19:54:36:  43000000 
INFO  @ Thu, 19 May 2016 19:54:38:  44000000 
INFO  @ Thu, 19 May 2016 19:54:40:  45000000 
INFO  @ Thu, 19 May 2016 19:54:43:  46000000 
INFO  @ Thu, 19 May 2016 19:54:45:  47000000 
INFO  @ Thu, 19 May 2016 19:54:47:  48000000 
INFO  @ Thu, 19 May 2016 19:54:49:  49000000 
INFO  @ Thu, 19 May 2016 19:54:51:  50000000 
INFO  @ Thu, 19 May 2016 19:54:53:  51000000 
INFO  @ Thu, 19 May 2016 19:54:55:  52000000 
INFO  @ Thu, 19 May 2016 19:54:57:  53000000 
INFO  @ Thu, 19 May 2016 19:54:59:  54000000 
INFO  @ Thu, 19 May 2016 19:55:02:  55000000 
INFO  @ Thu, 19 May 2016 19:55:04:  56000000 
INFO  @ Thu, 19 May 2016 19:55:06:  57000000 
INFO  @ Thu, 19 May 2016 19:55:08:  58000000 
INFO  @ Thu, 19 May 2016 19:55:10:  59000000 
INFO  @ Thu, 19 May 2016 19:55:12:  60000000 
INFO  @ Thu, 19 May 2016 19:55:14:  61000000 
INFO  @ Thu, 19 May 2016 19:55:16:  62000000 
INFO  @ Thu, 19 May 2016 19:55:18:  63000000 
INFO  @ Thu, 19 May 2016 19:55:21:  64000000 
INFO  @ Thu, 19 May 2016 19:55:23:  65000000 
INFO  @ Thu, 19 May 2016 19:55:25:  66000000 
INFO  @ Thu, 19 May 2016 19:55:27:  67000000 
INFO  @ Thu, 19 May 2016 19:55:29:  68000000 
INFO  @ Thu, 19 May 2016 19:55:31:  69000000 
INFO  @ Thu, 19 May 2016 19:55:33:  70000000 
INFO  @ Thu, 19 May 2016 19:55:35:  71000000 
INFO  @ Thu, 19 May 2016 19:55:37:  72000000 
INFO  @ Thu, 19 May 2016 19:55:40:  73000000 
INFO  @ Thu, 19 May 2016 19:55:42:  74000000 
INFO  @ Thu, 19 May 2016 19:55:44:  75000000 
INFO  @ Thu, 19 May 2016 19:55:46:  76000000 
INFO  @ Thu, 19 May 2016 19:55:48:  77000000 
INFO  @ Thu, 19 May 2016 19:55:50:  78000000 
INFO  @ Thu, 19 May 2016 19:55:52:  79000000 
INFO  @ Thu, 19 May 2016 19:55:54:  80000000 
INFO  @ Thu, 19 May 2016 19:55:56:  81000000 
INFO  @ Thu, 19 May 2016 19:55:58:  82000000 
INFO  @ Thu, 19 May 2016 19:56:01:  83000000 
INFO  @ Thu, 19 May 2016 19:56:03:  84000000 
INFO  @ Thu, 19 May 2016 19:56:05:  85000000 
INFO  @ Thu, 19 May 2016 19:56:07:  86000000 
INFO  @ Thu, 19 May 2016 19:56:09:  87000000 
INFO  @ Thu, 19 May 2016 19:56:11:  88000000 
INFO  @ Thu, 19 May 2016 19:56:13:  89000000 
INFO  @ Thu, 19 May 2016 19:56:15:  90000000 
INFO  @ Thu, 19 May 2016 19:56:17:  91000000 
INFO  @ Thu, 19 May 2016 19:56:25: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 19:56:25: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 19:56:25: #1  total tags in treatment: 91060218 
INFO  @ Thu, 19 May 2016 19:56:25: #1 finished! 
INFO  @ Thu, 19 May 2016 19:56:25: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:56:25: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:56:25: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:56:25: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:56:25: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:56:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:56:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:59:54: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 20:04:08: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 20:04:11: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 20:04:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 20:04:15: Done! 
INFO  @ Thu, 19 May 2016 20:04:24: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 20:04:24: #1 read tag files... 
INFO  @ Thu, 19 May 2016 20:04:24: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 20:04:26:  1000000 
INFO  @ Thu, 19 May 2016 20:04:28:  2000000 
INFO  @ Thu, 19 May 2016 20:04:30:  3000000 
INFO  @ Thu, 19 May 2016 20:04:32:  4000000 
INFO  @ Thu, 19 May 2016 20:04:34:  5000000 
INFO  @ Thu, 19 May 2016 20:04:36:  6000000 
INFO  @ Thu, 19 May 2016 20:04:38:  7000000 
INFO  @ Thu, 19 May 2016 20:04:40:  8000000 
INFO  @ Thu, 19 May 2016 20:04:42:  9000000 
INFO  @ Thu, 19 May 2016 20:04:44:  10000000 
INFO  @ Thu, 19 May 2016 20:04:46:  11000000 
INFO  @ Thu, 19 May 2016 20:04:48:  12000000 
INFO  @ Thu, 19 May 2016 20:04:50:  13000000 
INFO  @ Thu, 19 May 2016 20:04:52:  14000000 
INFO  @ Thu, 19 May 2016 20:04:54:  15000000 
INFO  @ Thu, 19 May 2016 20:04:56:  16000000 
INFO  @ Thu, 19 May 2016 20:04:58:  17000000 
INFO  @ Thu, 19 May 2016 20:05:00:  18000000 
INFO  @ Thu, 19 May 2016 20:05:02:  19000000 
INFO  @ Thu, 19 May 2016 20:05:04:  20000000 
INFO  @ Thu, 19 May 2016 20:05:06:  21000000 
INFO  @ Thu, 19 May 2016 20:05:07:  22000000 
INFO  @ Thu, 19 May 2016 20:05:09:  23000000 
INFO  @ Thu, 19 May 2016 20:05:11:  24000000 
INFO  @ Thu, 19 May 2016 20:05:13:  25000000 
INFO  @ Thu, 19 May 2016 20:05:15:  26000000 
INFO  @ Thu, 19 May 2016 20:05:17:  27000000 
INFO  @ Thu, 19 May 2016 20:05:19:  28000000 
INFO  @ Thu, 19 May 2016 20:05:21:  29000000 
INFO  @ Thu, 19 May 2016 20:05:23:  30000000 
INFO  @ Thu, 19 May 2016 20:05:25:  31000000 
INFO  @ Thu, 19 May 2016 20:05:27:  32000000 
INFO  @ Thu, 19 May 2016 20:05:29:  33000000 
INFO  @ Thu, 19 May 2016 20:05:31:  34000000 
INFO  @ Thu, 19 May 2016 20:05:33:  35000000 
INFO  @ Thu, 19 May 2016 20:05:35:  36000000 
INFO  @ Thu, 19 May 2016 20:05:37:  37000000 
INFO  @ Thu, 19 May 2016 20:05:39:  38000000 
INFO  @ Thu, 19 May 2016 20:05:40:  39000000 
INFO  @ Thu, 19 May 2016 20:05:42:  40000000 
INFO  @ Thu, 19 May 2016 20:05:44:  41000000 
INFO  @ Thu, 19 May 2016 20:05:46:  42000000 
INFO  @ Thu, 19 May 2016 20:05:48:  43000000 
INFO  @ Thu, 19 May 2016 20:05:50:  44000000 
INFO  @ Thu, 19 May 2016 20:05:52:  45000000 
INFO  @ Thu, 19 May 2016 20:05:54:  46000000 
INFO  @ Thu, 19 May 2016 20:05:56:  47000000 
INFO  @ Thu, 19 May 2016 20:05:58:  48000000 
INFO  @ Thu, 19 May 2016 20:06:00:  49000000 
INFO  @ Thu, 19 May 2016 20:06:02:  50000000 
INFO  @ Thu, 19 May 2016 20:06:04:  51000000 
INFO  @ Thu, 19 May 2016 20:06:05:  52000000 
INFO  @ Thu, 19 May 2016 20:06:07:  53000000 
INFO  @ Thu, 19 May 2016 20:06:09:  54000000 
INFO  @ Thu, 19 May 2016 20:06:11:  55000000 
INFO  @ Thu, 19 May 2016 20:06:13:  56000000 
INFO  @ Thu, 19 May 2016 20:06:15:  57000000 
INFO  @ Thu, 19 May 2016 20:06:17:  58000000 
INFO  @ Thu, 19 May 2016 20:06:19:  59000000 
INFO  @ Thu, 19 May 2016 20:06:21:  60000000 
INFO  @ Thu, 19 May 2016 20:06:23:  61000000 
INFO  @ Thu, 19 May 2016 20:06:25:  62000000 
INFO  @ Thu, 19 May 2016 20:06:27:  63000000 
INFO  @ Thu, 19 May 2016 20:06:29:  64000000 
INFO  @ Thu, 19 May 2016 20:06:30:  65000000 
INFO  @ Thu, 19 May 2016 20:06:32:  66000000 
INFO  @ Thu, 19 May 2016 20:06:34:  67000000 
INFO  @ Thu, 19 May 2016 20:06:36:  68000000 
INFO  @ Thu, 19 May 2016 20:06:38:  69000000 
INFO  @ Thu, 19 May 2016 20:06:40:  70000000 
INFO  @ Thu, 19 May 2016 20:06:42:  71000000 
INFO  @ Thu, 19 May 2016 20:06:44:  72000000 
INFO  @ Thu, 19 May 2016 20:06:46:  73000000 
INFO  @ Thu, 19 May 2016 20:06:47:  74000000 
INFO  @ Thu, 19 May 2016 20:06:49:  75000000 
INFO  @ Thu, 19 May 2016 20:06:51:  76000000 
INFO  @ Thu, 19 May 2016 20:06:53:  77000000 
INFO  @ Thu, 19 May 2016 20:06:55:  78000000 
INFO  @ Thu, 19 May 2016 20:06:57:  79000000 
INFO  @ Thu, 19 May 2016 20:06:59:  80000000 
INFO  @ Thu, 19 May 2016 20:07:01:  81000000 
INFO  @ Thu, 19 May 2016 20:07:03:  82000000 
INFO  @ Thu, 19 May 2016 20:07:04:  83000000 
INFO  @ Thu, 19 May 2016 20:07:06:  84000000 
INFO  @ Thu, 19 May 2016 20:07:08:  85000000 
INFO  @ Thu, 19 May 2016 20:07:10:  86000000 
INFO  @ Thu, 19 May 2016 20:07:12:  87000000 
INFO  @ Thu, 19 May 2016 20:07:14:  88000000 
INFO  @ Thu, 19 May 2016 20:07:16:  89000000 
INFO  @ Thu, 19 May 2016 20:07:18:  90000000 
INFO  @ Thu, 19 May 2016 20:07:20:  91000000 
INFO  @ Thu, 19 May 2016 20:07:27: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 20:07:27: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 20:07:27: #1  total tags in treatment: 91060218 
INFO  @ Thu, 19 May 2016 20:07:27: #1 finished! 
INFO  @ Thu, 19 May 2016 20:07:27: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 20:07:27: #2 Skipped... 
INFO  @ Thu, 19 May 2016 20:07:27: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 20:07:27: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 20:07:27: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 20:07:27: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 20:07:27: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 20:07:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 20:10:51: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 20:10:51: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 20:10:51: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 20:10:51: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 20:10:51: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 20:22:44: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 20:22:50: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 20:22:54: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 20:22:56: Done!

Num	35
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_40
Name	macs2_atac pooled
Thread	thread_Root
PID	46459

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

Start	2016-05-19 19:53:02
End	2016-05-19 21:32:59
Elapsed	01:39:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.gappedPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:53:05: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:53:07:  1000000 
INFO  @ Thu, 19 May 2016 19:53:09:  2000000 
INFO  @ Thu, 19 May 2016 19:53:11:  3000000 
INFO  @ Thu, 19 May 2016 19:53:13:  4000000 
INFO  @ Thu, 19 May 2016 19:53:15:  5000000 
INFO  @ Thu, 19 May 2016 19:53:17:  6000000 
INFO  @ Thu, 19 May 2016 19:53:19:  7000000 
INFO  @ Thu, 19 May 2016 19:53:21:  8000000 
INFO  @ Thu, 19 May 2016 19:53:23:  9000000 
INFO  @ Thu, 19 May 2016 19:53:25:  10000000 
INFO  @ Thu, 19 May 2016 19:53:27:  11000000 
INFO  @ Thu, 19 May 2016 19:53:29:  12000000 
INFO  @ Thu, 19 May 2016 19:53:31:  13000000 
INFO  @ Thu, 19 May 2016 19:53:33:  14000000 
INFO  @ Thu, 19 May 2016 19:53:35:  15000000 
INFO  @ Thu, 19 May 2016 19:53:37:  16000000 
INFO  @ Thu, 19 May 2016 19:53:39:  17000000 
INFO  @ Thu, 19 May 2016 19:53:41:  18000000 
INFO  @ Thu, 19 May 2016 19:53:43:  19000000 
INFO  @ Thu, 19 May 2016 19:53:45:  20000000 
INFO  @ Thu, 19 May 2016 19:53:47:  21000000 
INFO  @ Thu, 19 May 2016 19:53:49:  22000000 
INFO  @ Thu, 19 May 2016 19:53:51:  23000000 
INFO  @ Thu, 19 May 2016 19:53:53:  24000000 
INFO  @ Thu, 19 May 2016 19:53:55:  25000000 
INFO  @ Thu, 19 May 2016 19:53:57:  26000000 
INFO  @ Thu, 19 May 2016 19:53:59:  27000000 
INFO  @ Thu, 19 May 2016 19:54:01:  28000000 
INFO  @ Thu, 19 May 2016 19:54:03:  29000000 
INFO  @ Thu, 19 May 2016 19:54:05:  30000000 
INFO  @ Thu, 19 May 2016 19:54:07:  31000000 
INFO  @ Thu, 19 May 2016 19:54:09:  32000000 
INFO  @ Thu, 19 May 2016 19:54:12:  33000000 
INFO  @ Thu, 19 May 2016 19:54:14:  34000000 
INFO  @ Thu, 19 May 2016 19:54:16:  35000000 
INFO  @ Thu, 19 May 2016 19:54:18:  36000000 
INFO  @ Thu, 19 May 2016 19:54:20:  37000000 
INFO  @ Thu, 19 May 2016 19:54:22:  38000000 
INFO  @ Thu, 19 May 2016 19:54:24:  39000000 
INFO  @ Thu, 19 May 2016 19:54:26:  40000000 
INFO  @ Thu, 19 May 2016 19:54:28:  41000000 
INFO  @ Thu, 19 May 2016 19:54:30:  42000000 
INFO  @ Thu, 19 May 2016 19:54:32:  43000000 
INFO  @ Thu, 19 May 2016 19:54:34:  44000000 
INFO  @ Thu, 19 May 2016 19:54:36:  45000000 
INFO  @ Thu, 19 May 2016 19:54:38:  46000000 
INFO  @ Thu, 19 May 2016 19:54:40:  47000000 
INFO  @ Thu, 19 May 2016 19:54:42:  48000000 
INFO  @ Thu, 19 May 2016 19:54:44:  49000000 
INFO  @ Thu, 19 May 2016 19:54:46:  50000000 
INFO  @ Thu, 19 May 2016 19:54:48:  51000000 
INFO  @ Thu, 19 May 2016 19:54:50:  52000000 
INFO  @ Thu, 19 May 2016 19:54:52:  53000000 
INFO  @ Thu, 19 May 2016 19:54:54:  54000000 
INFO  @ Thu, 19 May 2016 19:54:56:  55000000 
INFO  @ Thu, 19 May 2016 19:54:58:  56000000 
INFO  @ Thu, 19 May 2016 19:55:00:  57000000 
INFO  @ Thu, 19 May 2016 19:55:02:  58000000 
INFO  @ Thu, 19 May 2016 19:55:04:  59000000 
INFO  @ Thu, 19 May 2016 19:55:06:  60000000 
INFO  @ Thu, 19 May 2016 19:55:08:  61000000 
INFO  @ Thu, 19 May 2016 19:55:10:  62000000 
INFO  @ Thu, 19 May 2016 19:55:12:  63000000 
INFO  @ Thu, 19 May 2016 19:55:14:  64000000 
INFO  @ Thu, 19 May 2016 19:55:16:  65000000 
INFO  @ Thu, 19 May 2016 19:55:18:  66000000 
INFO  @ Thu, 19 May 2016 19:55:20:  67000000 
INFO  @ Thu, 19 May 2016 19:55:22:  68000000 
INFO  @ Thu, 19 May 2016 19:55:24:  69000000 
INFO  @ Thu, 19 May 2016 19:55:26:  70000000 
INFO  @ Thu, 19 May 2016 19:55:28:  71000000 
INFO  @ Thu, 19 May 2016 19:55:30:  72000000 
INFO  @ Thu, 19 May 2016 19:55:32:  73000000 
INFO  @ Thu, 19 May 2016 19:55:34:  74000000 
INFO  @ Thu, 19 May 2016 19:55:36:  75000000 
INFO  @ Thu, 19 May 2016 19:55:38:  76000000 
INFO  @ Thu, 19 May 2016 19:55:40:  77000000 
INFO  @ Thu, 19 May 2016 19:55:42:  78000000 
INFO  @ Thu, 19 May 2016 19:55:44:  79000000 
INFO  @ Thu, 19 May 2016 19:55:46:  80000000 
INFO  @ Thu, 19 May 2016 19:55:48:  81000000 
INFO  @ Thu, 19 May 2016 19:55:50:  82000000 
INFO  @ Thu, 19 May 2016 19:55:52:  83000000 
INFO  @ Thu, 19 May 2016 19:55:54:  84000000 
INFO  @ Thu, 19 May 2016 19:55:56:  85000000 
INFO  @ Thu, 19 May 2016 19:55:58:  86000000 
INFO  @ Thu, 19 May 2016 19:56:00:  87000000 
INFO  @ Thu, 19 May 2016 19:56:02:  88000000 
INFO  @ Thu, 19 May 2016 19:56:04:  89000000 
INFO  @ Thu, 19 May 2016 19:56:06:  90000000 
INFO  @ Thu, 19 May 2016 19:56:08:  91000000 
INFO  @ Thu, 19 May 2016 19:56:16: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 19:56:16: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 19:56:16: #1  total tags in treatment: 91060218 
INFO  @ Thu, 19 May 2016 19:56:16: #1 finished! 
INFO  @ Thu, 19 May 2016 19:56:16: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:56:16: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:56:16: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:56:16: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:56:16: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:56:16: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:56:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:59:47: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 20:03:36: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.xls 
INFO  @ Thu, 19 May 2016 20:03:39: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 20:03:41: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 20:03:42: Done! 
INFO  @ Thu, 19 May 2016 20:03:52: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 20:03:52: #1 read tag files... 
INFO  @ Thu, 19 May 2016 20:03:52: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 20:03:54:  1000000 
INFO  @ Thu, 19 May 2016 20:03:55:  2000000 
INFO  @ Thu, 19 May 2016 20:03:57:  3000000 
INFO  @ Thu, 19 May 2016 20:03:59:  4000000 
INFO  @ Thu, 19 May 2016 20:04:01:  5000000 
INFO  @ Thu, 19 May 2016 20:04:03:  6000000 
INFO  @ Thu, 19 May 2016 20:04:05:  7000000 
INFO  @ Thu, 19 May 2016 20:04:07:  8000000 
INFO  @ Thu, 19 May 2016 20:04:09:  9000000 
INFO  @ Thu, 19 May 2016 20:04:11:  10000000 
INFO  @ Thu, 19 May 2016 20:04:13:  11000000 
INFO  @ Thu, 19 May 2016 20:04:15:  12000000 
INFO  @ Thu, 19 May 2016 20:04:17:  13000000 
INFO  @ Thu, 19 May 2016 20:04:19:  14000000 
INFO  @ Thu, 19 May 2016 20:04:21:  15000000 
INFO  @ Thu, 19 May 2016 20:04:23:  16000000 
INFO  @ Thu, 19 May 2016 20:04:25:  17000000 
INFO  @ Thu, 19 May 2016 20:04:27:  18000000 
INFO  @ Thu, 19 May 2016 20:04:29:  19000000 
INFO  @ Thu, 19 May 2016 20:04:31:  20000000 
INFO  @ Thu, 19 May 2016 20:04:33:  21000000 
INFO  @ Thu, 19 May 2016 20:04:35:  22000000 
INFO  @ Thu, 19 May 2016 20:04:37:  23000000 
INFO  @ Thu, 19 May 2016 20:04:39:  24000000 
INFO  @ Thu, 19 May 2016 20:04:41:  25000000 
INFO  @ Thu, 19 May 2016 20:04:43:  26000000 
INFO  @ Thu, 19 May 2016 20:04:45:  27000000 
INFO  @ Thu, 19 May 2016 20:04:47:  28000000 
INFO  @ Thu, 19 May 2016 20:04:49:  29000000 
INFO  @ Thu, 19 May 2016 20:04:51:  30000000 
INFO  @ Thu, 19 May 2016 20:04:52:  31000000 
INFO  @ Thu, 19 May 2016 20:04:54:  32000000 
INFO  @ Thu, 19 May 2016 20:04:56:  33000000 
INFO  @ Thu, 19 May 2016 20:04:58:  34000000 
INFO  @ Thu, 19 May 2016 20:05:00:  35000000 
INFO  @ Thu, 19 May 2016 20:05:02:  36000000 
INFO  @ Thu, 19 May 2016 20:05:04:  37000000 
INFO  @ Thu, 19 May 2016 20:05:06:  38000000 
INFO  @ Thu, 19 May 2016 20:05:08:  39000000 
INFO  @ Thu, 19 May 2016 20:05:10:  40000000 
INFO  @ Thu, 19 May 2016 20:05:12:  41000000 
INFO  @ Thu, 19 May 2016 20:05:14:  42000000 
INFO  @ Thu, 19 May 2016 20:05:15:  43000000 
INFO  @ Thu, 19 May 2016 20:05:17:  44000000 
INFO  @ Thu, 19 May 2016 20:05:19:  45000000 
INFO  @ Thu, 19 May 2016 20:05:21:  46000000 
INFO  @ Thu, 19 May 2016 20:05:23:  47000000 
INFO  @ Thu, 19 May 2016 20:05:25:  48000000 
INFO  @ Thu, 19 May 2016 20:05:27:  49000000 
INFO  @ Thu, 19 May 2016 20:05:29:  50000000 
INFO  @ Thu, 19 May 2016 20:05:31:  51000000 
INFO  @ Thu, 19 May 2016 20:05:33:  52000000 
INFO  @ Thu, 19 May 2016 20:05:34:  53000000 
INFO  @ Thu, 19 May 2016 20:05:36:  54000000 
INFO  @ Thu, 19 May 2016 20:05:38:  55000000 
INFO  @ Thu, 19 May 2016 20:05:40:  56000000 
INFO  @ Thu, 19 May 2016 20:05:42:  57000000 
INFO  @ Thu, 19 May 2016 20:05:44:  58000000 
INFO  @ Thu, 19 May 2016 20:05:46:  59000000 
INFO  @ Thu, 19 May 2016 20:05:48:  60000000 
INFO  @ Thu, 19 May 2016 20:05:50:  61000000 
INFO  @ Thu, 19 May 2016 20:05:51:  62000000 
INFO  @ Thu, 19 May 2016 20:05:53:  63000000 
INFO  @ Thu, 19 May 2016 20:05:55:  64000000 
INFO  @ Thu, 19 May 2016 20:05:57:  65000000 
INFO  @ Thu, 19 May 2016 20:05:59:  66000000 
INFO  @ Thu, 19 May 2016 20:06:01:  67000000 
INFO  @ Thu, 19 May 2016 20:06:03:  68000000 
INFO  @ Thu, 19 May 2016 20:06:05:  69000000 
INFO  @ Thu, 19 May 2016 20:06:07:  70000000 
INFO  @ Thu, 19 May 2016 20:06:09:  71000000 
INFO  @ Thu, 19 May 2016 20:06:11:  72000000 
INFO  @ Thu, 19 May 2016 20:06:13:  73000000 
INFO  @ Thu, 19 May 2016 20:06:15:  74000000 
INFO  @ Thu, 19 May 2016 20:06:17:  75000000 
INFO  @ Thu, 19 May 2016 20:06:18:  76000000 
INFO  @ Thu, 19 May 2016 20:06:20:  77000000 
INFO  @ Thu, 19 May 2016 20:06:22:  78000000 
INFO  @ Thu, 19 May 2016 20:06:24:  79000000 
INFO  @ Thu, 19 May 2016 20:06:26:  80000000 
INFO  @ Thu, 19 May 2016 20:06:28:  81000000 
INFO  @ Thu, 19 May 2016 20:06:30:  82000000 
INFO  @ Thu, 19 May 2016 20:06:32:  83000000 
INFO  @ Thu, 19 May 2016 20:06:34:  84000000 
INFO  @ Thu, 19 May 2016 20:06:36:  85000000 
INFO  @ Thu, 19 May 2016 20:06:37:  86000000 
INFO  @ Thu, 19 May 2016 20:06:39:  87000000 
INFO  @ Thu, 19 May 2016 20:06:41:  88000000 
INFO  @ Thu, 19 May 2016 20:06:43:  89000000 
INFO  @ Thu, 19 May 2016 20:06:45:  90000000 
INFO  @ Thu, 19 May 2016 20:06:47:  91000000 
INFO  @ Thu, 19 May 2016 20:06:54: #1 tag size is determined as 65 bps 
INFO  @ Thu, 19 May 2016 20:06:54: #1 tag size = 65 
INFO  @ Thu, 19 May 2016 20:06:54: #1  total tags in treatment: 91060218 
INFO  @ Thu, 19 May 2016 20:06:54: #1 finished! 
INFO  @ Thu, 19 May 2016 20:06:54: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 20:06:54: #2 Skipped... 
INFO  @ Thu, 19 May 2016 20:06:54: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 20:06:54: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 20:06:54: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 20:06:54: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 20:06:54: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 19 May 2016 20:06:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 20:10:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 20:10:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 20:10:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 20:10:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 20:10:24: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 20:21:12: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.xls 
INFO  @ Thu, 19 May 2016 20:21:15: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 20:21:18: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_summits.bed 
INFO  @ Thu, 19 May 2016 20:21:20: Done! 
INFO  @ Thu, 19 May 2016 20:21:25: Read and build treatment bedGraph... 
INFO  @ Thu, 19 May 2016 20:24:12: Read and build control bedGraph... 
INFO  @ Thu, 19 May 2016 20:25:09: Build scoreTrackII... 
INFO  @ Thu, 19 May 2016 20:26:21: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 19 May 2016 20:35:45: Write bedGraph of scores... 
INFO  @ Thu, 19 May 2016 20:41:06: Finished 'FE'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_FE.bdg'! 
INFO  @ Thu, 19 May 2016 20:55:20: Read and build treatment bedGraph... 
INFO  @ Thu, 19 May 2016 20:58:07: Read and build control bedGraph... 
INFO  @ Thu, 19 May 2016 20:59:09: Build scoreTrackII... 
INFO  @ Thu, 19 May 2016 21:01:50: Values in your input bedGraph files will be multiplied by 91.060218 ... 
INFO  @ Thu, 19 May 2016 21:12:53: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 19 May 2016 21:14:32: Write bedGraph of scores... 
INFO  @ Thu, 19 May 2016 21:18:53: Finished 'ppois'! Please check '/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	46469

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

Start	2016-05-19 19:53:02
End	2016-05-19 20:12:31
Elapsed	00:19:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:53:05: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:53:07:  1000000 
INFO  @ Thu, 19 May 2016 19:53:09:  2000000 
INFO  @ Thu, 19 May 2016 19:53:11:  3000000 
INFO  @ Thu, 19 May 2016 19:53:13:  4000000 
INFO  @ Thu, 19 May 2016 19:53:15:  5000000 
INFO  @ Thu, 19 May 2016 19:53:17:  6000000 
INFO  @ Thu, 19 May 2016 19:53:19:  7000000 
INFO  @ Thu, 19 May 2016 19:53:21:  8000000 
INFO  @ Thu, 19 May 2016 19:53:23:  9000000 
INFO  @ Thu, 19 May 2016 19:53:25:  10000000 
INFO  @ Thu, 19 May 2016 19:53:27:  11000000 
INFO  @ Thu, 19 May 2016 19:53:29:  12000000 
INFO  @ Thu, 19 May 2016 19:53:31:  13000000 
INFO  @ Thu, 19 May 2016 19:53:33:  14000000 
INFO  @ Thu, 19 May 2016 19:53:35:  15000000 
INFO  @ Thu, 19 May 2016 19:53:37:  16000000 
INFO  @ Thu, 19 May 2016 19:53:40:  17000000 
INFO  @ Thu, 19 May 2016 19:53:42:  18000000 
INFO  @ Thu, 19 May 2016 19:53:44:  19000000 
INFO  @ Thu, 19 May 2016 19:53:46:  20000000 
INFO  @ Thu, 19 May 2016 19:53:48:  21000000 
INFO  @ Thu, 19 May 2016 19:53:50:  22000000 
INFO  @ Thu, 19 May 2016 19:53:52:  23000000 
INFO  @ Thu, 19 May 2016 19:53:54:  24000000 
INFO  @ Thu, 19 May 2016 19:53:56:  25000000 
INFO  @ Thu, 19 May 2016 19:53:58:  26000000 
INFO  @ Thu, 19 May 2016 19:54:00:  27000000 
INFO  @ Thu, 19 May 2016 19:54:02:  28000000 
INFO  @ Thu, 19 May 2016 19:54:04:  29000000 
INFO  @ Thu, 19 May 2016 19:54:06:  30000000 
INFO  @ Thu, 19 May 2016 19:54:08:  31000000 
INFO  @ Thu, 19 May 2016 19:54:10:  32000000 
INFO  @ Thu, 19 May 2016 19:54:12:  33000000 
INFO  @ Thu, 19 May 2016 19:54:14:  34000000 
INFO  @ Thu, 19 May 2016 19:54:16:  35000000 
INFO  @ Thu, 19 May 2016 19:54:18:  36000000 
INFO  @ Thu, 19 May 2016 19:54:20:  37000000 
INFO  @ Thu, 19 May 2016 19:54:22:  38000000 
INFO  @ Thu, 19 May 2016 19:54:24:  39000000 
INFO  @ Thu, 19 May 2016 19:54:26:  40000000 
INFO  @ Thu, 19 May 2016 19:54:28:  41000000 
INFO  @ Thu, 19 May 2016 19:54:30:  42000000 
INFO  @ Thu, 19 May 2016 19:54:32:  43000000 
INFO  @ Thu, 19 May 2016 19:54:34:  44000000 
INFO  @ Thu, 19 May 2016 19:54:36:  45000000 
INFO  @ Thu, 19 May 2016 19:54:38:  46000000 
INFO  @ Thu, 19 May 2016 19:54:40:  47000000 
INFO  @ Thu, 19 May 2016 19:54:42:  48000000 
INFO  @ Thu, 19 May 2016 19:54:44:  49000000 
INFO  @ Thu, 19 May 2016 19:54:49: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 19:54:49: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 19:54:49: #1  total tags in treatment: 49496536 
INFO  @ Thu, 19 May 2016 19:54:49: #1 finished! 
INFO  @ Thu, 19 May 2016 19:54:49: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:54:49: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:54:49: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:54:49: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:54:49: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:54:49: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:54:49: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:57:14: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:59:57: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 20:00:00: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 20:00:02: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 20:00:04: Done! 
INFO  @ Thu, 19 May 2016 20:00:13: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 20:00:13: #1 read tag files... 
INFO  @ Thu, 19 May 2016 20:00:13: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 20:00:16:  1000000 
INFO  @ Thu, 19 May 2016 20:00:17:  2000000 
INFO  @ Thu, 19 May 2016 20:00:19:  3000000 
INFO  @ Thu, 19 May 2016 20:00:21:  4000000 
INFO  @ Thu, 19 May 2016 20:00:23:  5000000 
INFO  @ Thu, 19 May 2016 20:00:25:  6000000 
INFO  @ Thu, 19 May 2016 20:00:27:  7000000 
INFO  @ Thu, 19 May 2016 20:00:29:  8000000 
INFO  @ Thu, 19 May 2016 20:00:31:  9000000 
INFO  @ Thu, 19 May 2016 20:00:33:  10000000 
INFO  @ Thu, 19 May 2016 20:00:35:  11000000 
INFO  @ Thu, 19 May 2016 20:00:37:  12000000 
INFO  @ Thu, 19 May 2016 20:00:39:  13000000 
INFO  @ Thu, 19 May 2016 20:00:41:  14000000 
INFO  @ Thu, 19 May 2016 20:00:43:  15000000 
INFO  @ Thu, 19 May 2016 20:00:45:  16000000 
INFO  @ Thu, 19 May 2016 20:00:47:  17000000 
INFO  @ Thu, 19 May 2016 20:00:49:  18000000 
INFO  @ Thu, 19 May 2016 20:00:51:  19000000 
INFO  @ Thu, 19 May 2016 20:00:52:  20000000 
INFO  @ Thu, 19 May 2016 20:00:54:  21000000 
INFO  @ Thu, 19 May 2016 20:00:56:  22000000 
INFO  @ Thu, 19 May 2016 20:00:58:  23000000 
INFO  @ Thu, 19 May 2016 20:01:00:  24000000 
INFO  @ Thu, 19 May 2016 20:01:02:  25000000 
INFO  @ Thu, 19 May 2016 20:01:04:  26000000 
INFO  @ Thu, 19 May 2016 20:01:06:  27000000 
INFO  @ Thu, 19 May 2016 20:01:08:  28000000 
INFO  @ Thu, 19 May 2016 20:01:10:  29000000 
INFO  @ Thu, 19 May 2016 20:01:11:  30000000 
INFO  @ Thu, 19 May 2016 20:01:13:  31000000 
INFO  @ Thu, 19 May 2016 20:01:15:  32000000 
INFO  @ Thu, 19 May 2016 20:01:17:  33000000 
INFO  @ Thu, 19 May 2016 20:01:19:  34000000 
INFO  @ Thu, 19 May 2016 20:01:21:  35000000 
INFO  @ Thu, 19 May 2016 20:01:23:  36000000 
INFO  @ Thu, 19 May 2016 20:01:25:  37000000 
INFO  @ Thu, 19 May 2016 20:01:27:  38000000 
INFO  @ Thu, 19 May 2016 20:01:29:  39000000 
INFO  @ Thu, 19 May 2016 20:01:31:  40000000 
INFO  @ Thu, 19 May 2016 20:01:33:  41000000 
INFO  @ Thu, 19 May 2016 20:01:35:  42000000 
INFO  @ Thu, 19 May 2016 20:01:37:  43000000 
INFO  @ Thu, 19 May 2016 20:01:39:  44000000 
INFO  @ Thu, 19 May 2016 20:01:40:  45000000 
INFO  @ Thu, 19 May 2016 20:01:42:  46000000 
INFO  @ Thu, 19 May 2016 20:01:44:  47000000 
INFO  @ Thu, 19 May 2016 20:01:46:  48000000 
INFO  @ Thu, 19 May 2016 20:01:48:  49000000 
INFO  @ Thu, 19 May 2016 20:01:53: #1 tag size is determined as 70 bps 
INFO  @ Thu, 19 May 2016 20:01:53: #1 tag size = 70 
INFO  @ Thu, 19 May 2016 20:01:53: #1  total tags in treatment: 49496536 
INFO  @ Thu, 19 May 2016 20:01:53: #1 finished! 
INFO  @ Thu, 19 May 2016 20:01:53: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 20:01:53: #2 Skipped... 
INFO  @ Thu, 19 May 2016 20:01:53: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 20:01:53: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 20:01:53: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 20:01:53: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 20:01:53: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 20:01:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 20:04:18: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 20:04:18: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 20:04:18: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 20:04:18: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 20:04:18: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 20:12:16: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 20:12:21: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 20:12:25: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 20:12:27: 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	46490

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

Start	2016-05-19 19:53:02
End	2016-05-19 20:12:36
Elapsed	00:19:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 19:53:05: #1 read tag files... 
INFO  @ Thu, 19 May 2016 19:53:05: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 19:53:07:  1000000 
INFO  @ Thu, 19 May 2016 19:53:09:  2000000 
INFO  @ Thu, 19 May 2016 19:53:11:  3000000 
INFO  @ Thu, 19 May 2016 19:53:13:  4000000 
INFO  @ Thu, 19 May 2016 19:53:15:  5000000 
INFO  @ Thu, 19 May 2016 19:53:17:  6000000 
INFO  @ Thu, 19 May 2016 19:53:19:  7000000 
INFO  @ Thu, 19 May 2016 19:53:21:  8000000 
INFO  @ Thu, 19 May 2016 19:53:24:  9000000 
INFO  @ Thu, 19 May 2016 19:53:26:  10000000 
INFO  @ Thu, 19 May 2016 19:53:28:  11000000 
INFO  @ Thu, 19 May 2016 19:53:30:  12000000 
INFO  @ Thu, 19 May 2016 19:53:32:  13000000 
INFO  @ Thu, 19 May 2016 19:53:34:  14000000 
INFO  @ Thu, 19 May 2016 19:53:36:  15000000 
INFO  @ Thu, 19 May 2016 19:53:38:  16000000 
INFO  @ Thu, 19 May 2016 19:53:40:  17000000 
INFO  @ Thu, 19 May 2016 19:53:42:  18000000 
INFO  @ Thu, 19 May 2016 19:53:44:  19000000 
INFO  @ Thu, 19 May 2016 19:53:46:  20000000 
INFO  @ Thu, 19 May 2016 19:53:48:  21000000 
INFO  @ Thu, 19 May 2016 19:53:50:  22000000 
INFO  @ Thu, 19 May 2016 19:53:52:  23000000 
INFO  @ Thu, 19 May 2016 19:53:54:  24000000 
INFO  @ Thu, 19 May 2016 19:53:56:  25000000 
INFO  @ Thu, 19 May 2016 19:53:58:  26000000 
INFO  @ Thu, 19 May 2016 19:54:00:  27000000 
INFO  @ Thu, 19 May 2016 19:54:03:  28000000 
INFO  @ Thu, 19 May 2016 19:54:05:  29000000 
INFO  @ Thu, 19 May 2016 19:54:07:  30000000 
INFO  @ Thu, 19 May 2016 19:54:09:  31000000 
INFO  @ Thu, 19 May 2016 19:54:11:  32000000 
INFO  @ Thu, 19 May 2016 19:54:13:  33000000 
INFO  @ Thu, 19 May 2016 19:54:15:  34000000 
INFO  @ Thu, 19 May 2016 19:54:17:  35000000 
INFO  @ Thu, 19 May 2016 19:54:19:  36000000 
INFO  @ Thu, 19 May 2016 19:54:21:  37000000 
INFO  @ Thu, 19 May 2016 19:54:23:  38000000 
INFO  @ Thu, 19 May 2016 19:54:25:  39000000 
INFO  @ Thu, 19 May 2016 19:54:27:  40000000 
INFO  @ Thu, 19 May 2016 19:54:29:  41000000 
INFO  @ Thu, 19 May 2016 19:54:31:  42000000 
INFO  @ Thu, 19 May 2016 19:54:33:  43000000 
INFO  @ Thu, 19 May 2016 19:54:35:  44000000 
INFO  @ Thu, 19 May 2016 19:54:37:  45000000 
INFO  @ Thu, 19 May 2016 19:54:39:  46000000 
INFO  @ Thu, 19 May 2016 19:54:41:  47000000 
INFO  @ Thu, 19 May 2016 19:54:43:  48000000 
INFO  @ Thu, 19 May 2016 19:54:45:  49000000 
INFO  @ Thu, 19 May 2016 19:54:50: #1 tag size is determined as 63 bps 
INFO  @ Thu, 19 May 2016 19:54:50: #1 tag size = 63 
INFO  @ Thu, 19 May 2016 19:54:50: #1  total tags in treatment: 49496534 
INFO  @ Thu, 19 May 2016 19:54:50: #1 finished! 
INFO  @ Thu, 19 May 2016 19:54:50: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 19:54:50: #2 Skipped... 
INFO  @ Thu, 19 May 2016 19:54:50: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 19:54:50: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 19:54:50: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 19:54:50: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Thu, 19 May 2016 19:54:50: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 19:57:14: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 19:59:54: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 19:59:56: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Thu, 19 May 2016 19:59:58: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Thu, 19 May 2016 20:00:00: Done! 
INFO  @ Thu, 19 May 2016 20:00:10: 
# Command line: callpeak -t /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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  @ Thu, 19 May 2016 20:00:10: #1 read tag files... 
INFO  @ Thu, 19 May 2016 20:00:10: #1 read treatment tags... 
INFO  @ Thu, 19 May 2016 20:00:12:  1000000 
INFO  @ Thu, 19 May 2016 20:00:14:  2000000 
INFO  @ Thu, 19 May 2016 20:00:15:  3000000 
INFO  @ Thu, 19 May 2016 20:00:17:  4000000 
INFO  @ Thu, 19 May 2016 20:00:19:  5000000 
INFO  @ Thu, 19 May 2016 20:00:21:  6000000 
INFO  @ Thu, 19 May 2016 20:00:23:  7000000 
INFO  @ Thu, 19 May 2016 20:00:25:  8000000 
INFO  @ Thu, 19 May 2016 20:00:27:  9000000 
INFO  @ Thu, 19 May 2016 20:00:29:  10000000 
INFO  @ Thu, 19 May 2016 20:00:31:  11000000 
INFO  @ Thu, 19 May 2016 20:00:33:  12000000 
INFO  @ Thu, 19 May 2016 20:00:35:  13000000 
INFO  @ Thu, 19 May 2016 20:00:37:  14000000 
INFO  @ Thu, 19 May 2016 20:00:39:  15000000 
INFO  @ Thu, 19 May 2016 20:00:41:  16000000 
INFO  @ Thu, 19 May 2016 20:00:43:  17000000 
INFO  @ Thu, 19 May 2016 20:00:45:  18000000 
INFO  @ Thu, 19 May 2016 20:00:46:  19000000 
INFO  @ Thu, 19 May 2016 20:00:48:  20000000 
INFO  @ Thu, 19 May 2016 20:00:50:  21000000 
INFO  @ Thu, 19 May 2016 20:00:52:  22000000 
INFO  @ Thu, 19 May 2016 20:00:54:  23000000 
INFO  @ Thu, 19 May 2016 20:00:56:  24000000 
INFO  @ Thu, 19 May 2016 20:00:58:  25000000 
INFO  @ Thu, 19 May 2016 20:01:00:  26000000 
INFO  @ Thu, 19 May 2016 20:01:02:  27000000 
INFO  @ Thu, 19 May 2016 20:01:03:  28000000 
INFO  @ Thu, 19 May 2016 20:01:05:  29000000 
INFO  @ Thu, 19 May 2016 20:01:07:  30000000 
INFO  @ Thu, 19 May 2016 20:01:09:  31000000 
INFO  @ Thu, 19 May 2016 20:01:11:  32000000 
INFO  @ Thu, 19 May 2016 20:01:13:  33000000 
INFO  @ Thu, 19 May 2016 20:01:15:  34000000 
INFO  @ Thu, 19 May 2016 20:01:17:  35000000 
INFO  @ Thu, 19 May 2016 20:01:18:  36000000 
INFO  @ Thu, 19 May 2016 20:01:20:  37000000 
INFO  @ Thu, 19 May 2016 20:01:22:  38000000 
INFO  @ Thu, 19 May 2016 20:01:24:  39000000 
INFO  @ Thu, 19 May 2016 20:01:26:  40000000 
INFO  @ Thu, 19 May 2016 20:01:28:  41000000 
INFO  @ Thu, 19 May 2016 20:01:30:  42000000 
INFO  @ Thu, 19 May 2016 20:01:32:  43000000 
INFO  @ Thu, 19 May 2016 20:01:34:  44000000 
INFO  @ Thu, 19 May 2016 20:01:36:  45000000 
INFO  @ Thu, 19 May 2016 20:01:38:  46000000 
INFO  @ Thu, 19 May 2016 20:01:40:  47000000 
INFO  @ Thu, 19 May 2016 20:01:42:  48000000 
INFO  @ Thu, 19 May 2016 20:01:43:  49000000 
INFO  @ Thu, 19 May 2016 20:01:48: #1 tag size is determined as 63 bps 
INFO  @ Thu, 19 May 2016 20:01:48: #1 tag size = 63 
INFO  @ Thu, 19 May 2016 20:01:48: #1  total tags in treatment: 49496534 
INFO  @ Thu, 19 May 2016 20:01:48: #1 finished! 
INFO  @ Thu, 19 May 2016 20:01:48: #2 Build Peak Model... 
INFO  @ Thu, 19 May 2016 20:01:48: #2 Skipped... 
INFO  @ Thu, 19 May 2016 20:01:48: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Thu, 19 May 2016 20:01:48: #2 Use 150 as fragment length 
INFO  @ Thu, 19 May 2016 20:01:48: #3 Call peaks... 
INFO  @ Thu, 19 May 2016 20:01:48: #3 Going to call summits inside each peak ... 
INFO  @ Thu, 19 May 2016 20:01:48: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Thu, 19 May 2016 20:01:48: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 19 May 2016 20:04:12: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 19 May 2016 20:04:12: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Thu, 19 May 2016 20:04:12: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Thu, 19 May 2016 20:04:12: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 19 May 2016 20:04:12: #3 Call peaks for each chromosome... 
INFO  @ Thu, 19 May 2016 20:12:21: #4 Write output xls file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Thu, 19 May 2016 20:12:26: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Thu, 19 May 2016 20:12:29: #4 Write summits bed file... /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Thu, 19 May 2016 20:12:31: Done!

Num	38
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_43
Name	filt_top_peaks rep1
Thread	thread_Root
PID	42705

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:09
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42707

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:09
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42709

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:10
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42711

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:10
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42713

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:10
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42715

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:10
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42717

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:09
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42719

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42721

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42723

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42725

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42727

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42729

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:10
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42731

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:07
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42733

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42735

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42737

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:08
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	42739

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

Start	2016-05-19 21:33:00
End	2016-05-19 21:33:07
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	43809

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

Start	2016-05-19 21:33:11
End	2016-05-19 21:33:12
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	24619451	24619729	Peak_2	33757	.	32.82161	3375.78540	3367.55835	135
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz has inconsistent naming convention for record:
mm9_chr1	24619812	24620100	Peak_2	56177	.	38.95545	5617.74365	5609.21533	143
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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:
chrM	14665	16612	Peak_2	47982	.	2.70523	4798.21777	4790.53857	1097
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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:
chrM	14671	16636	Peak_2	48579	.	2.71668	4857.95898	4850.22559	1096

Num	57
ID	task.callpeak_etc.naive_overlap_thresh_gpeak.line_125.id_62
Name	naive_overlap_thresh gpeak
Thread	thread_Root
PID	43814

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

Start	2016-05-19 21:33:11
End	2016-05-19 21:33:12
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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	197138782	197139464	Peak_132653	61	.	197138782	197139464	0	2	1,1	0,681	2.14919	7.14516	6.12303
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	197170403	197170772	Peak_342660	5	.	197170403	197170772	0	2	1,1	0,368	1.07641	1.45273	0.57649
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	197102522	197102782	Peak_272823	8	.	197102522	197102782	0	2	1,1	0,259	1.63261	1.93299	0.85823
ERROR: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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	197140460	197140634	Peak_166897	35	.	197140460	197140634	0	1	174	0	2.11939	4.59630	3.54733

Num	58
ID	task.idr.idr2_rep1_rep2.line_72.id_63
Name	idr2 rep1-rep2
Thread	thread_Root
PID	43827

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

Start	2016-05-19 21:33:11
End	2016-05-19 21:41:34
Elapsed	00:08:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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]
Final parameter values: [1.30 0.80 0.63 0.42]
Number of reported peaks - 389379/389379 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 182774/389379 (46.9%)

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3084614	3086138	.	812	.	1.39499	3.60391	1.86860	1002	1.63	1.96	0

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3084614	3086138	.	812	.	1.39499	3.60391	1.86860	1002	1.63	1.96	0

Num	59
ID	task.idr.idr2_rep1_pr.line_72.id_64
Name	idr2 rep1-pr
Thread	thread_Root
PID	43837

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

Start	2016-05-19 21:33:11
End	2016-05-19 21:40:20
Elapsed	00:07:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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]
Final parameter values: [1.65 0.73 0.85 0.38]
Number of reported peaks - 377649/377649 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 190722/377649 (50.5%)

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3079020	3080121	.	506	.	1.47021	3.57223	1.74203	1004	0.50	1.22	0

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3079020	3080121	.	506	.	1.47021	3.57223	1.74203	1004	0.50	1.22	0

Num	60
ID	task.idr.idr2_rep2_pr.line_72.id_65
Name	idr2 rep2-pr
Thread	thread_Root
PID	43850

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

Start	2016-05-19 21:33:11
End	2016-05-19 21:40:23
Elapsed	00:07:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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]
Final parameter values: [1.64 0.73 0.84 0.39]
Number of reported peaks - 364884/364884 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 194402/364884 (53.3%)

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	87408943	87409453	.	1000	.	1.47037	2.42634	0.69789	434	2.05	2.51	0

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	87408943	87409453	.	1000	.	1.47037	2.42634	0.69789	434	2.05	2.51	0

Num	61
ID	task.idr.idr2_ppr.line_72.id_66
Name	idr2 ppr
Thread	thread_Root
PID	43858

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

Start	2016-05-19 21:33:11
End	2016-05-19 21:41:17
Elapsed	00:08:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt.png /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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_noMultiMap_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_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_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]
Final parameter values: [1.79 0.68 0.89 0.41]
Number of reported peaks - 415569/415569 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 252472/415569 (60.8%)

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3084614	3086138	.	1000	.	1.39499	3.60391	1.86860	1002	2.69	3.09	0

***** WARNING: File /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3084614	3086138	.	1000	.	1.39499	3.60391	1.86860	1002	2.69	3.09	0

Num	62
ID	task.base.line_414.id_75
Name	task.base.line_414.id_75
Thread	thread_Root
PID	47500

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

Start	2016-05-19 21:41:35
End	2016-05-19 21:41:35
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	63
ID	task.base.line_414.id_76
Name	task.base.line_414.id_76
Thread	thread_Root
PID	47505

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

Start	2016-05-19 21:41:35
End	2016-05-19 21:41:35
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	64
ID	task.base.line_414.id_77
Name	task.base.line_414.id_77
Thread	thread_Root
PID	47515

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

Start	2016-05-19 21:41:35
End	2016-05-19 21:41:35
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.12-col.bed.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.12-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.12-col.bed.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	65
ID	task.base.line_414.id_78
Name	task.base.line_414.id_78
Thread	thread_Root
PID	47527

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

Start	2016-05-19 21:41:35
End	2016-05-19 21:41:35
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	66
ID	task.idr.idr_final_qc.line_210.id_79
Name	idr final qc
Thread	thread_Root
PID	47548

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

Start	2016-05-19 21:41:36
End	2016-05-19 21:41:37
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/IDR_final.qc
Dependencies

 
# SYS command. line 212

 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 214

 echo -e "Nt\tN1	N2	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/IDR_final.qc

# SYS command. line 215

 echo -e "183666\t191195	194835	""252882\trep1-rep2\tpooled_pseudo_rep\t1.3768579922250173\t1.0190381547634615\t1" >> /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/IDR_final.qc

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

Num	67
ID	task.atac.ataqc_rep1.line_861.id_80
Name	ataqc rep1
Thread	thread_142
PID	47553

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	1
Mem

Start	2016-05-19 21:41:36
End	2016-05-19 21:41:36
Elapsed	00:00:00
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 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE_qc.html /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE_qc.txt
Dependencies

 
# SYS command. line 863

 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 867

 export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"

# SYS command. line 869

 cd /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1

# SYS command. line 871

 /srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
		    --workdir /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1 \
		    --outdir /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1 \
		    --outprefix 3hr_rep2_merged_R1.trim.PE2SE \
		    --genome hg19 \
		    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
		    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
		    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
		    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
		    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
		    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
		    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
		    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
		    --pbc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc\
		    --fastq1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz --fastq2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz \
		    --alignedbam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam \
		    --alignmentlog /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log \
		    --coordsortbam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam \
		    --duplog /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc \
		    --finalbam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam \
		    --finalbed /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
		    --bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
		    --peaks /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
		    --naive_overlap_peaks /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
		    --idr_peaks /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
Traceback (most recent call last):
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1519, in 
    main()
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1315, in main
    chr_m_reads, fraction_chr_m = get_chr_m(COORDSORT_BAM)
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 160, in get_chr_m
    tot_reads += int(chrom_stats[2])
IndexError: list index out of range

Num	68
ID	task.atac.ataqc_rep2.line_861.id_81
Name	ataqc rep2
Thread	thread_143
PID	47561

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	1
Mem

Start	2016-05-19 21:41:36
End	2016-05-19 21:41:36
Elapsed	00:00:00
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 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE_qc.html /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE_qc.txt
Dependencies

 
# SYS command. line 863

 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 867

 export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"

# SYS command. line 869

 cd /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2

# SYS command. line 871

 /srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
		    --workdir /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2 \
		    --outdir /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2 \
		    --outprefix 3hr_rep3_merged_R1.trim.PE2SE \
		    --genome hg19 \
		    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
		    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
		    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
		    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
		    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
		    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
		    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
		    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
		    --pbc /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc\
		    --fastq1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz --fastq2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz \
		    --alignedbam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam \
		    --alignmentlog /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log \
		    --coordsortbam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam \
		    --duplog /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc \
		    --finalbam /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam \
		    --finalbed /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
		    --bigwig /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
		    --peaks /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
		    --naive_overlap_peaks /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
		    --idr_peaks /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
Traceback (most recent call last):
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1519, in 
    main()
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1315, in main
    chr_m_reads, fraction_chr_m = get_chr_m(COORDSORT_BAM)
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 160, in get_chr_m
    tot_reads += int(chrom_stats[2])
IndexError: list index out of range

Type	Name	Value
string	_	/bin/sh
string	_JAVA_OPTIONS	-Xms256M -Xmx512M -XX:ParallelGCThreads=1
bool	allowEmpty	false
string[]	args	[-out_dir, 4x_experiments/baseChroms_noMultiMap_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, -par_lvl, 5, -nth_bwt2, 6]
string	BASSETDIR	/srv/scratch/annashch/Basset
bool	canFail	false
int	cpus	1
int	cpusLocal	48
string	CRC	/srv/scratch/annashch/crc
int	day	86400
string	DEEPLEARN_SCRIPTS_DIR	/srv/scratch/annashch/deeplearning_avanti
string	DEEPLIFT_DIR	/srv/scratch/annashch/deeplift/deeplift
real	E	2.718281828459045
string	EIGEN	/mnt/lab_data/montgomery/shared/Eigen
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/annashch/enhancer_prediction_code
int	G	1073741824
string	HOME	/users/annashch/
int	hour	3600
int	K	1024
string	KERAS_DIR	/users/annashch/keras
string	KRB5CCNAME	FILE:/tmp/krb5cc_1091_nRCEqi
string	LANG	en_US.UTF-8
string	LD_LIBRARY_PATH	/lib/x86_64-linux-gnu:/usr/local/cudnn/lib64:
string	LOADEDMODULES
string	LOGNAME	annashch
string	LUACPATH	/srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:
string	LUAPATH	/srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:
int	M	1048576
string	MAIL	/var/mail/annashch
string	MALLOC_ARENA_MAX	4
string	MAX_JAVA_MEM	20G
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	node
string	OLDPWD	/srv/scratch/annashch/output/4x_experiments
int	P	1125899906842624
string	PATH	/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin
real	PI	3.141592653589793
string	ppwd	/srv/scratch/annashch/output
string	programName	atac.bds
string	programPath	/srv/scratch/annashch/bds_atac/atac.bds
string	PWD	/srv/scratch/annashch/output
string	PYTHONPATH	/users/annashch/keras:/srv/scratch/annashch/Basset/src:/users/annashch/keras:/srv/scratch/annashch/Basset/src:
string	QT_QPA_PLATFORMTHEME	appmenu-qt5
string	queue
int	retry	0
string	SHELL	/bin/bash
string	SHLVL	2
string	SSH_CLIENT	171.65.76.147 42019 22
string	SSH_CONNECTION	171.65.76.147 42019 171.65.76.162 22
string	SSH_TTY	/dev/pts/128
string	STY	7061.pts-128.kali
string	system	local
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#57:co#205:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:us=\\E[4m:ue=\\E[24m:so=\\E[3m:\\\n\t:se=\\E[23m:mb=\\E[5m:md=\\E[1m:mr=\\E[7m:me=\\E[m:ms:\\\n\t:Co#8:pa#64:AF=\\E[3%dm:AB=\\E[4%dm:op=\\E[39;49m:AX:\\\n\t:vb=\\Eg:G0:as=\\E(0:ae=\\E(B:\\\n\t:ac=\\140\\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{\|\|}}~~..--++,,hhII00:\\\n\t:po=\\E[5i:pf=\\E[4i:Km=\\E[M:k0=\\E[10~:k1=\\EOP:k2=\\EOQ:\\\n\t:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:F3=\\E[1;2P:F4=\\E[1;2Q:F5=\\E[1;2R:F6=\\E[1;2S:\\\n\t:F7=\\E[15;2~:F8=\\E[17;2~:F9=\\E[18;2~:FA=\\E[19;2~:kb=:\\\n\t:K2=\\EOE:kB=\\E[Z:kF=\\E[1;2B:kR=\\E[1;2A:4=\\E[3;2~:\\\n\t:7=\\E[1;2F:#2=\\E[1;2H:#3=\\E[2;2~:#4=\\E[1;2D:%c=\\E[6;2~:\\\n\t:%e=\\E[5;2~:%i=\\E[1;2C:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:\\\n\t:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:\\\n\t:kd=\\EOB:kr=\\EOC:kl=\\EOD:km:
int	timeout	-1
string	USER	annashch
string	UTIL_SCRIPTS_DIR	/srv/scratch/annashch/av_scripts
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1091
string	XDG_SESSION_ID	896

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope