Script file	/srv/scratch/annashch/bds_atac/atac.bds
Program ID	atac.bds.20160516_204338_160
Start time	2016-05-16 20:43:38
Run time	22:04:58.169
Tasks executed	70
Tasks failed	2
Tasks failed names	ataqc rep2 ataqc rep1
Arguments*	[-out_dir, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160516_204338_160/task.postalign_bed.pool_tag_reps.line_405.id_36 atac.bds.20160516_204338_160/task.postalign_bed.pool_tag_reps_pr1.line_405.id_37 atac.bds.20160516_204338_160/task.postalign_bed.pool_tag_reps_pr2.line_405.id_38 atac.bds.20160516_204338_160/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_39 atac.bds.20160516_204338_160/task.callpeak_macs2.macs2_atac_pooled.line_192.id_40 atac.bds.20160516_204338_160/task.callpeak_macs2.macs2_atac_ppr1.pval0.1.line_192.id_41 atac.bds.20160516_204338_160/task.callpeak_macs2.macs2_atac_ppr2.pval0.1.line_192.id_42 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_43 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_44 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_45 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_46 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_25.id_47 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_25.id_48 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_49 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_50 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_51 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_52 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep2_pr1.line_25.id_53 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_rep2_pr2.line_25.id_54 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_55 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_56 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_57 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_58 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_ppr1.line_25.id_59 atac.bds.20160516_204338_160/task.callpeak_etc.filt_top_peaks_ppr2.line_25.id_60 atac.bds.20160516_204338_160/task.callpeak_etc.naive_overlap_thresh_peak.line_125.id_61 atac.bds.20160516_204338_160/task.callpeak_etc.naive_overlap_thresh_gpeak.line_125.id_62 atac.bds.20160516_204338_160/task.idr.idr2_rep1_rep2.line_72.id_63 atac.bds.20160516_204338_160/task.idr.idr2_rep1_pr.line_72.id_64 atac.bds.20160516_204338_160/task.idr.idr2_rep2_pr.line_72.id_65 atac.bds.20160516_204338_160/task.idr.idr2_ppr.line_72.id_66 atac.bds.20160516_204338_160/task.base.line_414.id_75 atac.bds.20160516_204338_160/task.base.line_414.id_76 atac.bds.20160516_204338_160/task.base.line_414.id_77 atac.bds.20160516_204338_160/task.base.line_414.id_78 atac.bds.20160516_204338_160/task.idr.idr_final_qc.line_210.id_79
thread_21	thread_Root	atac.bds.20160516_204338_160_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_131.id_7 atac.bds.20160516_204338_160_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_12 atac.bds.20160516_204338_160_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_23 atac.bds.20160516_204338_160_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_24 atac.bds.20160516_204338_160_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_25 atac.bds.20160516_204338_160_parallel_21/task.postalign_bed.spr_PE_rep2.line_248.id_26 atac.bds.20160516_204338_160_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_27 atac.bds.20160516_204338_160_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_28 atac.bds.20160516_204338_160_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_29 atac.bds.20160516_204338_160_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_30 atac.bds.20160516_204338_160_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_31 atac.bds.20160516_204338_160_parallel_21/task.callpeak_macs2.macs2_atac_rep2_pr1.pval0.1.line_192.id_32 atac.bds.20160516_204338_160_parallel_21/task.callpeak_macs2.macs2_atac_rep2_pr2.pval0.1.line_192.id_33 atac.bds.20160516_204338_160_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_34 atac.bds.20160516_204338_160_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_35
thread_20	thread_Root	atac.bds.20160516_204338_160_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_131.id_6 atac.bds.20160516_204338_160_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160516_204338_160_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_9 atac.bds.20160516_204338_160_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10 atac.bds.20160516_204338_160_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_11 atac.bds.20160516_204338_160_parallel_20/task.postalign_bed.spr_PE_rep1.line_248.id_13 atac.bds.20160516_204338_160_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_14 atac.bds.20160516_204338_160_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_15 atac.bds.20160516_204338_160_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_16 atac.bds.20160516_204338_160_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_17 atac.bds.20160516_204338_160_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_18 atac.bds.20160516_204338_160_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr1.pval0.1.line_192.id_19 atac.bds.20160516_204338_160_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr2.pval0.1.line_192.id_20 atac.bds.20160516_204338_160_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_21 atac.bds.20160516_204338_160_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_22
thread_136	thread_Root	atac.bds.20160516_204338_160_parallel_136/task.postalign_bam.srt_bam_rep1.line_345.id_80 atac.bds.20160516_204338_160_parallel_136/task.atac.ataqc_rep1.line_847.id_82
thread_137	thread_Root	atac.bds.20160516_204338_160_parallel_137/task.postalign_bam.srt_bam_rep2.line_345.id_81 atac.bds.20160516_204338_160_parallel_137/task.atac.ataqc_rep2.line_847.id_83

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	7109

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

Start	2016-05-16 20:43:39
End	2016-05-17 05:50:17
Elapsed	09:06:37
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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized \
			-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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	7115

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

Start	2016-05-16 20:43:39
End	2016-05-17 09:38:08
Elapsed	12:54:28
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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized \
			-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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	42861

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

Start	2016-05-17 05:50:18
End	2016-05-17 09:05:52
Elapsed	03:15:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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
[Tue May 17 07:31:00 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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
[Tue May 17 07:31:00 PDT 2016] Executing as annashch@kali on Linux 3.19.0-25-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-17 07:31:00	MarkDuplicates	Start of doWork freeMemory: 254890736; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 07:31:00	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 07:31:00	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 07:31:07	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr10:128,004,957
INFO	2016-05-17 07:31:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:31:11	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr11:120,821,161
INFO	2016-05-17 07:31:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:31:16	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr12:104,850,442
INFO	2016-05-17 07:31:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:31:21	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    5s.  Last read position: chr14:45,784,878
INFO	2016-05-17 07:31:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:31:29	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    7s.  Last read position: chr15:79,803,621
INFO	2016-05-17 07:31:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:31:36	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    6s.  Last read position: chr17:33,543,018
INFO	2016-05-17 07:31:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:31:41	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    4s.  Last read position: chr19:7,894,879
INFO	2016-05-17 07:31:41	MarkDuplicates	Tracking 36 as yet unmatched pairs. 36 records in RAM.
INFO	2016-05-17 07:31:48	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    6s.  Last read position: chr1:57,332,562
INFO	2016-05-17 07:31:48	MarkDuplicates	Tracking 28 as yet unmatched pairs. 28 records in RAM.
INFO	2016-05-17 07:31:52	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    4s.  Last read position: chr1:201,504,810
INFO	2016-05-17 07:31:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:31:57	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    4s.  Last read position: chr21:29,960,087
INFO	2016-05-17 07:31:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:32:03	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    5s.  Last read position: chr2:66,757,020
INFO	2016-05-17 07:32:03	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 07:32:11	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    7s.  Last read position: chr2:209,228,364
INFO	2016-05-17 07:32:11	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 07:32:16	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    5s.  Last read position: chr3:93,718,240
INFO	2016-05-17 07:32:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:32:23	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    6s.  Last read position: chr4:15,915,364
INFO	2016-05-17 07:32:23	MarkDuplicates	Tracking 36 as yet unmatched pairs. 36 records in RAM.
INFO	2016-05-17 07:32:41	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:   18s.  Last read position: chr4:183,129,063
INFO	2016-05-17 07:32:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:32:46	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    4s.  Last read position: chr5:135,417,441
INFO	2016-05-17 07:32:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:32:51	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    4s.  Last read position: chr6:57,148,135
INFO	2016-05-17 07:32:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:32:56	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    5s.  Last read position: chr7:32,996,951
INFO	2016-05-17 07:32:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:33:02	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    5s.  Last read position: chr8:22,234,490
INFO	2016-05-17 07:33:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:33:09	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    7s.  Last read position: chr9:14,838,646
INFO	2016-05-17 07:33:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:33:14	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    4s.  Last read position: chrM:396
INFO	2016-05-17 07:33:14	MarkDuplicates	Tracking 30664 as yet unmatched pairs. 30664 records in RAM.
INFO	2016-05-17 07:33:18	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,356
INFO	2016-05-17 07:33:18	MarkDuplicates	Tracking 7502 as yet unmatched pairs. 7502 records in RAM.
INFO	2016-05-17 07:33:22	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,396
INFO	2016-05-17 07:33:22	MarkDuplicates	Tracking 24530 as yet unmatched pairs. 24530 records in RAM.
INFO	2016-05-17 07:33:26	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,354
INFO	2016-05-17 07:33:26	MarkDuplicates	Tracking 19494 as yet unmatched pairs. 19494 records in RAM.
INFO	2016-05-17 07:33:30	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,653
INFO	2016-05-17 07:33:30	MarkDuplicates	Tracking 14156 as yet unmatched pairs. 14156 records in RAM.
INFO	2016-05-17 07:33:37	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    7s.  Last read position: chrM:9,872
INFO	2016-05-17 07:33:37	MarkDuplicates	Tracking 44298 as yet unmatched pairs. 44298 records in RAM.
INFO	2016-05-17 07:33:41	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,465
INFO	2016-05-17 07:33:41	MarkDuplicates	Tracking 16470 as yet unmatched pairs. 16470 records in RAM.
INFO	2016-05-17 07:33:45	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,765
INFO	2016-05-17 07:33:45	MarkDuplicates	Tracking 10416 as yet unmatched pairs. 10416 records in RAM.
INFO	2016-05-17 07:33:53	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    7s.  Last read position: chrM:14,337
INFO	2016-05-17 07:33:53	MarkDuplicates	Tracking 10302 as yet unmatched pairs. 10302 records in RAM.
INFO	2016-05-17 07:34:08	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:   15s.  Last read position: chrM:15,559
INFO	2016-05-17 07:34:08	MarkDuplicates	Tracking 34968 as yet unmatched pairs. 34968 records in RAM.
INFO	2016-05-17 07:34:12	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    3s.  Last read position: chrX:20,614,437
INFO	2016-05-17 07:34:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:34:17	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr10:50,068,602
INFO	2016-05-17 07:34:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:34:22	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr10:119,939,740
INFO	2016-05-17 07:34:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:34:28	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr11:54,295,688
INFO	2016-05-17 07:34:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:34:33	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr11:102,610,915
INFO	2016-05-17 07:34:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:34:38	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr12:61,397,657
INFO	2016-05-17 07:34:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:34:42	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:17,223,379
INFO	2016-05-17 07:34:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:34:47	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:87,933,864
INFO	2016-05-17 07:34:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:34:52	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:47,030,837
INFO	2016-05-17 07:34:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:34:57	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:109,479,832
INFO	2016-05-17 07:34:57	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 07:35:01	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr15:63,924,797
INFO	2016-05-17 07:35:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:35:09	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr16:20,442,955
INFO	2016-05-17 07:35:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:35:13	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr16:94,751,300
INFO	2016-05-17 07:35:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:35:18	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr17:64,186,273
INFO	2016-05-17 07:35:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:35:27	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    9s.  Last read position: mm9_chr18:39,471,929
INFO	2016-05-17 07:35:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:35:32	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr19:5,013,394
INFO	2016-05-17 07:35:32	MarkDuplicates	Tracking 58 as yet unmatched pairs. 58 records in RAM.
INFO	2016-05-17 07:35:37	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr1:12,989,848
INFO	2016-05-17 07:35:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:35:42	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:88,207,595
INFO	2016-05-17 07:35:42	MarkDuplicates	Tracking 36 as yet unmatched pairs. 36 records in RAM.
INFO	2016-05-17 07:35:49	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr1:161,722,559
INFO	2016-05-17 07:35:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:35:53	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr2:28,320,166
INFO	2016-05-17 07:35:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:35:57	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr2:94,719,814
INFO	2016-05-17 07:35:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:36:02	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr2:157,244,476
INFO	2016-05-17 07:36:02	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 07:36:06	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr3:55,397,343
INFO	2016-05-17 07:36:06	MarkDuplicates	Tracking 24 as yet unmatched pairs. 24 records in RAM.
INFO	2016-05-17 07:36:11	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr3:122,068,423
INFO	2016-05-17 07:36:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:36:16	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr4:44,584,406
INFO	2016-05-17 07:36:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:36:20	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr4:121,814,858
INFO	2016-05-17 07:36:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:36:28	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    8s.  Last read position: mm9_chr5:31,333,790
INFO	2016-05-17 07:36:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:36:33	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr5:105,380,432
INFO	2016-05-17 07:36:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:36:48	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:   15s.  Last read position: mm9_chr6:7,623,543
INFO	2016-05-17 07:36:48	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 07:36:52	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:87,280,518
INFO	2016-05-17 07:36:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:36:57	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:149,075,438
INFO	2016-05-17 07:36:57	MarkDuplicates	Tracking 36 as yet unmatched pairs. 36 records in RAM.
INFO	2016-05-17 07:37:02	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:06:01s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr7:87,377,807
INFO	2016-05-17 07:37:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:37:06	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr7:148,027,012
INFO	2016-05-17 07:37:06	MarkDuplicates	Tracking 32 as yet unmatched pairs. 32 records in RAM.
INFO	2016-05-17 07:37:11	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr8:77,824,389
INFO	2016-05-17 07:37:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:37:17	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    6s.  Last read position: mm9_chr9:11,738,097
INFO	2016-05-17 07:37:17	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 07:37:21	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr9:72,767,328
INFO	2016-05-17 07:37:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:37:26	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:116
INFO	2016-05-17 07:37:26	MarkDuplicates	Tracking 26224 as yet unmatched pairs. 26224 records in RAM.
INFO	2016-05-17 07:37:30	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:756
INFO	2016-05-17 07:37:30	MarkDuplicates	Tracking 56302 as yet unmatched pairs. 56302 records in RAM.
INFO	2016-05-17 07:37:34	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,462
INFO	2016-05-17 07:37:34	MarkDuplicates	Tracking 72826 as yet unmatched pairs. 72826 records in RAM.
INFO	2016-05-17 07:37:38	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,301
INFO	2016-05-17 07:37:38	MarkDuplicates	Tracking 50528 as yet unmatched pairs. 50528 records in RAM.
INFO	2016-05-17 07:37:42	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,929
INFO	2016-05-17 07:37:42	MarkDuplicates	Tracking 33588 as yet unmatched pairs. 33588 records in RAM.
INFO	2016-05-17 07:37:46	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:3,545
INFO	2016-05-17 07:37:46	MarkDuplicates	Tracking 51694 as yet unmatched pairs. 51694 records in RAM.
INFO	2016-05-17 07:37:49	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,148
INFO	2016-05-17 07:37:49	MarkDuplicates	Tracking 50404 as yet unmatched pairs. 50404 records in RAM.
INFO	2016-05-17 07:37:59	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:    9s.  Last read position: mm9_chrM:5,141
INFO	2016-05-17 07:37:59	MarkDuplicates	Tracking 26732 as yet unmatched pairs. 26732 records in RAM.
INFO	2016-05-17 07:38:03	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:6,262
INFO	2016-05-17 07:38:03	MarkDuplicates	Tracking 30420 as yet unmatched pairs. 30420 records in RAM.
INFO	2016-05-17 07:38:07	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,434
INFO	2016-05-17 07:38:07	MarkDuplicates	Tracking 40202 as yet unmatched pairs. 40202 records in RAM.
INFO	2016-05-17 07:38:11	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:12,177
INFO	2016-05-17 07:38:11	MarkDuplicates	Tracking 48314 as yet unmatched pairs. 48314 records in RAM.
INFO	2016-05-17 07:38:15	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:12,878
INFO	2016-05-17 07:38:15	MarkDuplicates	Tracking 32652 as yet unmatched pairs. 32652 records in RAM.
INFO	2016-05-17 07:38:19	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,758
INFO	2016-05-17 07:38:19	MarkDuplicates	Tracking 50980 as yet unmatched pairs. 50980 records in RAM.
INFO	2016-05-17 07:38:23	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,578
INFO	2016-05-17 07:38:23	MarkDuplicates	Tracking 34418 as yet unmatched pairs. 34418 records in RAM.
INFO	2016-05-17 07:38:27	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,340
INFO	2016-05-17 07:38:27	MarkDuplicates	Tracking 22636 as yet unmatched pairs. 22636 records in RAM.
INFO	2016-05-17 07:38:31	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrX:71,259,633
INFO	2016-05-17 07:38:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:38:33	MarkDuplicates	Read 82575174 records. 0 pairs never matched.
INFO	2016-05-17 07:38:42	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2883162760; totalMemory: 2910846976; maxMemory: 3817865216
INFO	2016-05-17 07:38:42	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 07:38:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 07:38:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 07:39:23	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 07:39:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1926522080; totalMemory: 2908225536; maxMemory: 3817865216
INFO	2016-05-17 07:39:25	MarkDuplicates	Marking 28518822 records as duplicates.
INFO	2016-05-17 07:39:25	MarkDuplicates	Found 4838961 optical duplicate clusters.
INFO	2016-05-17 07:41:23	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:57s.  Time for last 10,000,000:  117s.  Last read position: chr21:29,960,087
INFO	2016-05-17 07:43:25	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:59s.  Time for last 10,000,000:  122s.  Last read position: chr9:14,838,646
INFO	2016-05-17 07:45:11	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:45s.  Time for last 10,000,000:  106s.  Last read position: chrM:15,559
INFO	2016-05-17 07:47:16	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:50s.  Time for last 10,000,000:  124s.  Last read position: mm9_chr14:109,479,832
INFO	2016-05-17 07:49:21	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:09:55s.  Time for last 10,000,000:  124s.  Last read position: mm9_chr2:28,320,166
INFO	2016-05-17 07:51:25	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:12:00s.  Time for last 10,000,000:  124s.  Last read position: mm9_chr6:87,280,518
INFO	2016-05-17 07:53:23	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:13:57s.  Time for last 10,000,000:  117s.  Last read position: mm9_chrM:2,301
INFO	2016-05-17 07:55:07	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:15:41s.  Time for last 10,000,000:  103s.  Last read position: mm9_chrM:14,578
INFO	2016-05-17 07:55:35	MarkDuplicates	Before output close freeMemory: 2958923552; totalMemory: 2989490176; maxMemory: 3817865216
INFO	2016-05-17 07:55:35	MarkDuplicates	After output close freeMemory: 2958922496; totalMemory: 2989490176; maxMemory: 3817865216
[Tue May 17 07:55:35 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 24.58 minutes.
Runtime.totalMemory()=2989490176
[bam_sort_core] merging from 34 files...

Num	4
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_9
Name	nmsrt_bam rep1
Thread	thread_20
PID	10826

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

Start	2016-05-17 09:05:52
End	2016-05-17 09:33:35
Elapsed	00:27:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	5
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10
Name	bam_to_bedpe rep1
Thread	thread_20
PID	19221

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

Start	2016-05-17 09:33:36
End	2016-05-17 09:36:54
Elapsed	00:03:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	6
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_11
Name	bedpe_to_tag rep1
Thread	thread_20
PID	20841

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

Start	2016-05-17 09:36:55
End	2016-05-17 09:39:53
Elapsed	00:02:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	7
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_12
Name	dedup_bam_PE rep2
Thread	thread_21
PID	20910

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

Start	2016-05-17 09:38:09
End	2016-05-17 13:54:04
Elapsed	04:15:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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
[Tue May 17 12:00:31 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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
[Tue May 17 12:00:31 PDT 2016] Executing as annashch@kali on Linux 3.19.0-25-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-17 12:00:31	MarkDuplicates	Start of doWork freeMemory: 254890736; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 12:00:31	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 12:00:31	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 12:00:36	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr11:69,591,865
INFO	2016-05-17 12:00:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:00:41	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    4s.  Last read position: chr12:124,705,009
INFO	2016-05-17 12:00:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:00:46	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    5s.  Last read position: chr15:51,742,502
INFO	2016-05-17 12:00:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:00:51	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    5s.  Last read position: chr17:62,252,275
INFO	2016-05-17 12:00:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:00:58	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    6s.  Last read position: chr1:12,508,867
INFO	2016-05-17 12:00:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:01:05	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    6s.  Last read position: chr1:209,553,788
INFO	2016-05-17 12:01:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 12:01:10	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    5s.  Last read position: chr2:25,265,011
INFO	2016-05-17 12:01:10	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-17 12:01:14	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    4s.  Last read position: chr2:227,072,633
INFO	2016-05-17 12:01:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:01:19	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    4s.  Last read position: chr3:171,526,948
INFO	2016-05-17 12:01:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:01:26	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    7s.  Last read position: chr5:10,896,341
INFO	2016-05-17 12:01:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:01:34	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    7s.  Last read position: chr6:30,294,991
INFO	2016-05-17 12:01:34	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 12:01:38	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    4s.  Last read position: chr7:87,563,753
INFO	2016-05-17 12:01:38	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 12:01:43	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    4s.  Last read position: chr8:141,601,716
INFO	2016-05-17 12:01:43	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 12:01:48	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:209
INFO	2016-05-17 12:01:48	MarkDuplicates	Tracking 19704 as yet unmatched pairs. 19704 records in RAM.
INFO	2016-05-17 12:02:05	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:   17s.  Last read position: chrM:1,023
INFO	2016-05-17 12:02:05	MarkDuplicates	Tracking 15682 as yet unmatched pairs. 15682 records in RAM.
INFO	2016-05-17 12:02:09	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,740
INFO	2016-05-17 12:02:09	MarkDuplicates	Tracking 34720 as yet unmatched pairs. 34720 records in RAM.
INFO	2016-05-17 12:02:15	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,530
INFO	2016-05-17 12:02:15	MarkDuplicates	Tracking 15038 as yet unmatched pairs. 15038 records in RAM.
INFO	2016-05-17 12:02:19	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,856
INFO	2016-05-17 12:02:19	MarkDuplicates	Tracking 85622 as yet unmatched pairs. 85622 records in RAM.
INFO	2016-05-17 12:02:24	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,215
INFO	2016-05-17 12:02:24	MarkDuplicates	Tracking 98192 as yet unmatched pairs. 98192 records in RAM.
INFO	2016-05-17 12:02:28	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,468
INFO	2016-05-17 12:02:28	MarkDuplicates	Tracking 25794 as yet unmatched pairs. 25794 records in RAM.
INFO	2016-05-17 12:02:33	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,784
INFO	2016-05-17 12:02:33	MarkDuplicates	Tracking 57626 as yet unmatched pairs. 57626 records in RAM.
INFO	2016-05-17 12:02:39	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    6s.  Last read position: chrM:4,786
INFO	2016-05-17 12:02:39	MarkDuplicates	Tracking 4434 as yet unmatched pairs. 4434 records in RAM.
INFO	2016-05-17 12:02:43	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,817
INFO	2016-05-17 12:02:43	MarkDuplicates	Tracking 9202 as yet unmatched pairs. 9202 records in RAM.
INFO	2016-05-17 12:02:47	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,481
INFO	2016-05-17 12:02:47	MarkDuplicates	Tracking 23198 as yet unmatched pairs. 23198 records in RAM.
INFO	2016-05-17 12:02:51	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,218
INFO	2016-05-17 12:02:51	MarkDuplicates	Tracking 15276 as yet unmatched pairs. 15276 records in RAM.
INFO	2016-05-17 12:02:58	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    6s.  Last read position: chrM:8,023
INFO	2016-05-17 12:02:58	MarkDuplicates	Tracking 14422 as yet unmatched pairs. 14422 records in RAM.
INFO	2016-05-17 12:03:01	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,148
INFO	2016-05-17 12:03:01	MarkDuplicates	Tracking 20416 as yet unmatched pairs. 20416 records in RAM.
INFO	2016-05-17 12:03:05	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    4s.  Last read position: chrM:9,825
INFO	2016-05-17 12:03:05	MarkDuplicates	Tracking 72678 as yet unmatched pairs. 72678 records in RAM.
INFO	2016-05-17 12:03:10	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,184
INFO	2016-05-17 12:03:10	MarkDuplicates	Tracking 37486 as yet unmatched pairs. 37486 records in RAM.
INFO	2016-05-17 12:03:26	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:   16s.  Last read position: chrM:10,631
INFO	2016-05-17 12:03:26	MarkDuplicates	Tracking 38412 as yet unmatched pairs. 38412 records in RAM.
INFO	2016-05-17 12:03:30	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,313
INFO	2016-05-17 12:03:30	MarkDuplicates	Tracking 47366 as yet unmatched pairs. 47366 records in RAM.
INFO	2016-05-17 12:03:33	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,838
INFO	2016-05-17 12:03:33	MarkDuplicates	Tracking 8984 as yet unmatched pairs. 8984 records in RAM.
INFO	2016-05-17 12:03:38	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,246
INFO	2016-05-17 12:03:38	MarkDuplicates	Tracking 48676 as yet unmatched pairs. 48676 records in RAM.
INFO	2016-05-17 12:03:42	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,619
INFO	2016-05-17 12:03:42	MarkDuplicates	Tracking 54504 as yet unmatched pairs. 54504 records in RAM.
INFO	2016-05-17 12:03:45	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,108
INFO	2016-05-17 12:03:45	MarkDuplicates	Tracking 23106 as yet unmatched pairs. 23106 records in RAM.
INFO	2016-05-17 12:03:49	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,647
INFO	2016-05-17 12:03:49	MarkDuplicates	Tracking 13520 as yet unmatched pairs. 13520 records in RAM.
INFO	2016-05-17 12:03:53	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,058
INFO	2016-05-17 12:03:53	MarkDuplicates	Tracking 33654 as yet unmatched pairs. 33654 records in RAM.
INFO	2016-05-17 12:03:58	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,833
INFO	2016-05-17 12:03:58	MarkDuplicates	Tracking 11630 as yet unmatched pairs. 11630 records in RAM.
INFO	2016-05-17 12:04:02	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,144
INFO	2016-05-17 12:04:02	MarkDuplicates	Tracking 59620 as yet unmatched pairs. 59620 records in RAM.
INFO	2016-05-17 12:04:06	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,469
INFO	2016-05-17 12:04:06	MarkDuplicates	Tracking 26348 as yet unmatched pairs. 26348 records in RAM.
INFO	2016-05-17 12:04:10	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,760
INFO	2016-05-17 12:04:10	MarkDuplicates	Tracking 42456 as yet unmatched pairs. 42456 records in RAM.
INFO	2016-05-17 12:04:14	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,192
INFO	2016-05-17 12:04:14	MarkDuplicates	Tracking 21698 as yet unmatched pairs. 21698 records in RAM.
INFO	2016-05-17 12:04:18	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    3s.  Last read position: chrX:31,804,729
INFO	2016-05-17 12:04:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:04:25	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr10:69,602,149
INFO	2016-05-17 12:04:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 12:04:34	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    9s.  Last read position: mm9_chr11:5,345,040
INFO	2016-05-17 12:04:34	MarkDuplicates	Tracking 18 as yet unmatched pairs. 18 records in RAM.
INFO	2016-05-17 12:04:39	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr11:80,242,886
INFO	2016-05-17 12:04:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 12:04:44	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr12:40,703,288
INFO	2016-05-17 12:04:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:04:48	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:3,781,423
INFO	2016-05-17 12:04:48	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 12:04:53	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr13:95,213,302
INFO	2016-05-17 12:04:53	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-17 12:04:57	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr14:67,807,336
INFO	2016-05-17 12:04:57	MarkDuplicates	Tracking 18 as yet unmatched pairs. 18 records in RAM.
INFO	2016-05-17 12:05:01	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr15:50,502,110
INFO	2016-05-17 12:05:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:05:09	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr16:22,857,536
INFO	2016-05-17 12:05:09	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 12:05:13	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr17:22,524,575
INFO	2016-05-17 12:05:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:05:17	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr17:91,837,622
INFO	2016-05-17 12:05:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:05:22	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr19:3,415,430
INFO	2016-05-17 12:05:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:05:26	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:55s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:24,619,938
INFO	2016-05-17 12:05:26	MarkDuplicates	Tracking 10688 as yet unmatched pairs. 10688 records in RAM.
INFO	2016-05-17 12:05:30	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:120,906,323
INFO	2016-05-17 12:05:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:05:34	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr1:193,700,025
INFO	2016-05-17 12:05:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:05:50	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:   15s.  Last read position: mm9_chr2:78,647,654
INFO	2016-05-17 12:05:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:05:54	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr2:153,066,979
INFO	2016-05-17 12:05:54	MarkDuplicates	Tracking 28 as yet unmatched pairs. 28 records in RAM.
INFO	2016-05-17 12:06:00	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    5s.  Last read position: mm9_chr3:65,915,428
INFO	2016-05-17 12:06:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:06:04	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr3:142,910,371
INFO	2016-05-17 12:06:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:06:09	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr4:86,701,821
INFO	2016-05-17 12:06:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:06:13	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr5:3,800,294
INFO	2016-05-17 12:06:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:06:18	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr5:100,310,906
INFO	2016-05-17 12:06:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:06:22	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:16,619,295
INFO	2016-05-17 12:06:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:06:26	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr6:107,851,135
INFO	2016-05-17 12:06:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:06:31	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr7:36,661,770
INFO	2016-05-17 12:06:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 12:06:38	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:06:07s.  Time for last 1,000,000:    7s.  Last read position: mm9_chr7:129,316,546
INFO	2016-05-17 12:06:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:06:43	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr8:72,330,007
INFO	2016-05-17 12:06:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:06:47	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr9:14,305,255
INFO	2016-05-17 12:06:47	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 12:06:52	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    4s.  Last read position: mm9_chr9:94,004,690
INFO	2016-05-17 12:06:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 12:06:55	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:126
INFO	2016-05-17 12:06:55	MarkDuplicates	Tracking 89802 as yet unmatched pairs. 89802 records in RAM.
INFO	2016-05-17 12:07:04	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:321
INFO	2016-05-17 12:07:04	MarkDuplicates	Tracking 137160 as yet unmatched pairs. 137160 records in RAM.
INFO	2016-05-17 12:07:08	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:545
INFO	2016-05-17 12:07:08	MarkDuplicates	Tracking 55106 as yet unmatched pairs. 55106 records in RAM.
INFO	2016-05-17 12:07:12	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:751
INFO	2016-05-17 12:07:12	MarkDuplicates	Tracking 98338 as yet unmatched pairs. 98338 records in RAM.
INFO	2016-05-17 12:07:16	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:960
INFO	2016-05-17 12:07:16	MarkDuplicates	Tracking 77868 as yet unmatched pairs. 77868 records in RAM.
INFO	2016-05-17 12:07:22	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:1,139
INFO	2016-05-17 12:07:22	MarkDuplicates	Tracking 106268 as yet unmatched pairs. 106268 records in RAM.
INFO	2016-05-17 12:07:26	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,376
INFO	2016-05-17 12:07:26	MarkDuplicates	Tracking 70412 as yet unmatched pairs. 70412 records in RAM.
INFO	2016-05-17 12:07:30	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:1,735
INFO	2016-05-17 12:07:30	MarkDuplicates	Tracking 57132 as yet unmatched pairs. 57132 records in RAM.
INFO	2016-05-17 12:07:33	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,011
INFO	2016-05-17 12:07:33	MarkDuplicates	Tracking 43624 as yet unmatched pairs. 43624 records in RAM.
INFO	2016-05-17 12:07:37	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,263
INFO	2016-05-17 12:07:37	MarkDuplicates	Tracking 130226 as yet unmatched pairs. 130226 records in RAM.
INFO	2016-05-17 12:07:41	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,510
INFO	2016-05-17 12:07:41	MarkDuplicates	Tracking 91758 as yet unmatched pairs. 91758 records in RAM.
INFO	2016-05-17 12:07:45	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:2,716
INFO	2016-05-17 12:07:45	MarkDuplicates	Tracking 63812 as yet unmatched pairs. 63812 records in RAM.
INFO	2016-05-17 12:07:49	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:2,891
INFO	2016-05-17 12:07:49	MarkDuplicates	Tracking 89198 as yet unmatched pairs. 89198 records in RAM.
INFO	2016-05-17 12:07:53	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:3,087
INFO	2016-05-17 12:07:53	MarkDuplicates	Tracking 83932 as yet unmatched pairs. 83932 records in RAM.
INFO	2016-05-17 12:08:02	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    8s.  Last read position: mm9_chrM:3,283
INFO	2016-05-17 12:08:02	MarkDuplicates	Tracking 50106 as yet unmatched pairs. 50106 records in RAM.
INFO	2016-05-17 12:08:06	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:07:35s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:3,483
INFO	2016-05-17 12:08:06	MarkDuplicates	Tracking 106340 as yet unmatched pairs. 106340 records in RAM.
INFO	2016-05-17 12:08:21	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:07:49s.  Time for last 1,000,000:   14s.  Last read position: mm9_chrM:3,644
INFO	2016-05-17 12:08:21	MarkDuplicates	Tracking 82958 as yet unmatched pairs. 82958 records in RAM.
INFO	2016-05-17 12:08:25	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:07:53s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:3,845
INFO	2016-05-17 12:08:25	MarkDuplicates	Tracking 85386 as yet unmatched pairs. 85386 records in RAM.
INFO	2016-05-17 12:08:29	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:4,035
INFO	2016-05-17 12:08:29	MarkDuplicates	Tracking 118552 as yet unmatched pairs. 118552 records in RAM.
INFO	2016-05-17 12:08:33	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:08:02s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:4,222
INFO	2016-05-17 12:08:33	MarkDuplicates	Tracking 66060 as yet unmatched pairs. 66060 records in RAM.
INFO	2016-05-17 12:08:37	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:08:06s.  Time for last 1,000,000:    4s.  Last read position: mm9_chrM:4,437
INFO	2016-05-17 12:08:37	MarkDuplicates	Tracking 89726 as yet unmatched pairs. 89726 records in RAM.
INFO	2016-05-17 12:08:41	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:08:10s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:4,695
INFO	2016-05-17 12:08:41	MarkDuplicates	Tracking 105464 as yet unmatched pairs. 105464 records in RAM.
INFO	2016-05-17 12:08:45	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,348
INFO	2016-05-17 12:08:45	MarkDuplicates	Tracking 36352 as yet unmatched pairs. 36352 records in RAM.
INFO	2016-05-17 12:08:48	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:08:17s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:5,780
INFO	2016-05-17 12:08:48	MarkDuplicates	Tracking 61910 as yet unmatched pairs. 61910 records in RAM.
INFO	2016-05-17 12:08:55	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    6s.  Last read position: mm9_chrM:6,102
INFO	2016-05-17 12:08:55	MarkDuplicates	Tracking 55168 as yet unmatched pairs. 55168 records in RAM.
INFO	2016-05-17 12:08:58	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:6,391
INFO	2016-05-17 12:08:58	MarkDuplicates	Tracking 37542 as yet unmatched pairs. 37542 records in RAM.
INFO	2016-05-17 12:09:02	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:08:30s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,130
INFO	2016-05-17 12:09:02	MarkDuplicates	Tracking 51102 as yet unmatched pairs. 51102 records in RAM.
INFO	2016-05-17 12:09:05	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:08:34s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,303
INFO	2016-05-17 12:09:05	MarkDuplicates	Tracking 171998 as yet unmatched pairs. 171998 records in RAM.
INFO	2016-05-17 12:09:09	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,509
INFO	2016-05-17 12:09:09	MarkDuplicates	Tracking 107232 as yet unmatched pairs. 107232 records in RAM.
INFO	2016-05-17 12:09:13	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:11,777
INFO	2016-05-17 12:09:13	MarkDuplicates	Tracking 68052 as yet unmatched pairs. 68052 records in RAM.
INFO	2016-05-17 12:09:20	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    7s.  Last read position: mm9_chrM:11,991
INFO	2016-05-17 12:09:20	MarkDuplicates	Tracking 118642 as yet unmatched pairs. 118642 records in RAM.
INFO	2016-05-17 12:09:24	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,169
INFO	2016-05-17 12:09:24	MarkDuplicates	Tracking 71732 as yet unmatched pairs. 71732 records in RAM.
INFO	2016-05-17 12:09:28	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:08:57s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,379
INFO	2016-05-17 12:09:28	MarkDuplicates	Tracking 77108 as yet unmatched pairs. 77108 records in RAM.
INFO	2016-05-17 12:09:31	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,653
INFO	2016-05-17 12:09:31	MarkDuplicates	Tracking 58006 as yet unmatched pairs. 58006 records in RAM.
INFO	2016-05-17 12:09:35	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:12,909
INFO	2016-05-17 12:09:35	MarkDuplicates	Tracking 33760 as yet unmatched pairs. 33760 records in RAM.
INFO	2016-05-17 12:09:41	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    5s.  Last read position: mm9_chrM:13,289
INFO	2016-05-17 12:09:41	MarkDuplicates	Tracking 57444 as yet unmatched pairs. 57444 records in RAM.
INFO	2016-05-17 12:09:44	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,542
INFO	2016-05-17 12:09:44	MarkDuplicates	Tracking 81364 as yet unmatched pairs. 81364 records in RAM.
INFO	2016-05-17 12:09:48	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:13,786
INFO	2016-05-17 12:09:48	MarkDuplicates	Tracking 55568 as yet unmatched pairs. 55568 records in RAM.
INFO	2016-05-17 12:09:51	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,185
INFO	2016-05-17 12:09:51	MarkDuplicates	Tracking 22936 as yet unmatched pairs. 22936 records in RAM.
INFO	2016-05-17 12:09:55	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,401
INFO	2016-05-17 12:09:55	MarkDuplicates	Tracking 71052 as yet unmatched pairs. 71052 records in RAM.
INFO	2016-05-17 12:09:59	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,619
INFO	2016-05-17 12:09:59	MarkDuplicates	Tracking 61000 as yet unmatched pairs. 61000 records in RAM.
INFO	2016-05-17 12:10:03	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:14,838
INFO	2016-05-17 12:10:03	MarkDuplicates	Tracking 79878 as yet unmatched pairs. 79878 records in RAM.
INFO	2016-05-17 12:10:06	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,130
INFO	2016-05-17 12:10:06	MarkDuplicates	Tracking 36388 as yet unmatched pairs. 36388 records in RAM.
INFO	2016-05-17 12:10:10	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,374
INFO	2016-05-17 12:10:10	MarkDuplicates	Tracking 60432 as yet unmatched pairs. 60432 records in RAM.
INFO	2016-05-17 12:10:14	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    3s.  Last read position: mm9_chrM:15,589
INFO	2016-05-17 12:10:14	MarkDuplicates	Tracking 67032 as yet unmatched pairs. 67032 records in RAM.
INFO	2016-05-17 12:10:31	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:   16s.  Last read position: mm9_chrM:16,200
INFO	2016-05-17 12:10:31	MarkDuplicates	Tracking 32884 as yet unmatched pairs. 32884 records in RAM.
INFO	2016-05-17 12:10:34	MarkDuplicates	Read 118782800 records. 0 pairs never matched.
INFO	2016-05-17 12:10:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3430874280; totalMemory: 3458203648; maxMemory: 3817865216
INFO	2016-05-17 12:10:35	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 12:10:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 12:11:09	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 12:11:40	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 12:11:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2438822880; totalMemory: 3420979200; maxMemory: 3817865216
INFO	2016-05-17 12:11:44	MarkDuplicates	Marking 73822840 records as duplicates.
INFO	2016-05-17 12:11:44	MarkDuplicates	Found 22831370 optical duplicate clusters.
INFO	2016-05-17 12:13:37	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:51s.  Time for last 10,000,000:  111s.  Last read position: chr5:10,896,341
INFO	2016-05-17 12:15:17	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:31s.  Time for last 10,000,000:   99s.  Last read position: chrM:3,468
INFO	2016-05-17 12:16:47	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:01s.  Time for last 10,000,000:   89s.  Last read position: chrM:10,631
INFO	2016-05-17 12:18:19	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:33s.  Time for last 10,000,000:   92s.  Last read position: chrM:15,469
INFO	2016-05-17 12:20:08	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:22s.  Time for last 10,000,000:  108s.  Last read position: mm9_chr14:67,807,336
INFO	2016-05-17 12:22:06	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:20s.  Time for last 10,000,000:  118s.  Last read position: mm9_chr2:153,066,979
INFO	2016-05-17 12:24:06	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:12:20s.  Time for last 10,000,000:  120s.  Last read position: mm9_chr8:72,330,007
INFO	2016-05-17 12:25:46	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:14:00s.  Time for last 10,000,000:   99s.  Last read position: mm9_chrM:1,735
INFO	2016-05-17 12:27:22	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:15:36s.  Time for last 10,000,000:   95s.  Last read position: mm9_chrM:3,845
INFO	2016-05-17 12:28:55	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:17:09s.  Time for last 10,000,000:   93s.  Last read position: mm9_chrM:11,303
INFO	2016-05-17 12:30:31	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:18:45s.  Time for last 10,000,000:   95s.  Last read position: mm9_chrM:13,786
INFO	2016-05-17 12:31:57	MarkDuplicates	Before output close freeMemory: 3514142936; totalMemory: 3544711168; maxMemory: 3817865216
INFO	2016-05-17 12:31:57	MarkDuplicates	After output close freeMemory: 3514141880; totalMemory: 3544711168; maxMemory: 3817865216
[Tue May 17 12:31:57 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 31.43 minutes.
Runtime.totalMemory()=3544711168
[bam_sort_core] merging from 49 files...

Num	8
ID	task.postalign_bed.spr_PE_rep1.line_248.id_13
Name	spr_PE rep1
Thread	thread_20
PID	20993

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

Start	2016-05-17 09:39:54
End	2016-05-17 09:42:24
Elapsed	00:02:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.00" | \
			gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.01" | \
			gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22620

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

Start	2016-05-17 09:42:24
End	2016-05-17 09:44:08
Elapsed	00:01:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22622

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

Start	2016-05-17 09:42:25
End	2016-05-17 09:43:19
Elapsed	00:00:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22632

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

Start	2016-05-17 09:42:25
End	2016-05-17 09:43:20
Elapsed	00:00:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22854

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

Start	2016-05-17 09:44:09
End	2016-05-17 09:45:21
Elapsed	00:01:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	23628

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

Start	2016-05-17 09:45:22
End	2016-05-17 10:24:55
Elapsed	00:39:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmp7ZEBme/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign5d4b377ceac7
done. read 25000000 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1418811 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.226763430958829 
Top 3 estimates for fragment length 0 
Window half size 430 
Phantom peak location 80 
Phantom peak Correlation 0.2472056 
Normalized Strand cross-correlation coefficient (NSC) 1.598264 
Relative Strand Cross correlation Coefficient (RSC) 0.8059126 
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	23630

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

Start	2016-05-17 09:45:22
End	2016-05-17 10:00:25
Elapsed	00:15:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 09:45:27: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 09:45:27: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:45:27: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:45:29:  1000000 
INFO  @ Tue, 17 May 2016 09:45:31:  2000000 
INFO  @ Tue, 17 May 2016 09:45:33:  3000000 
INFO  @ Tue, 17 May 2016 09:45:35:  4000000 
INFO  @ Tue, 17 May 2016 09:45:37:  5000000 
INFO  @ Tue, 17 May 2016 09:45:39:  6000000 
INFO  @ Tue, 17 May 2016 09:45:41:  7000000 
INFO  @ Tue, 17 May 2016 09:45:43:  8000000 
INFO  @ Tue, 17 May 2016 09:45:45:  9000000 
INFO  @ Tue, 17 May 2016 09:45:47:  10000000 
INFO  @ Tue, 17 May 2016 09:45:49:  11000000 
INFO  @ Tue, 17 May 2016 09:45:51:  12000000 
INFO  @ Tue, 17 May 2016 09:45:53:  13000000 
INFO  @ Tue, 17 May 2016 09:45:55:  14000000 
INFO  @ Tue, 17 May 2016 09:45:57:  15000000 
INFO  @ Tue, 17 May 2016 09:45:59:  16000000 
INFO  @ Tue, 17 May 2016 09:46:01:  17000000 
INFO  @ Tue, 17 May 2016 09:46:03:  18000000 
INFO  @ Tue, 17 May 2016 09:46:05:  19000000 
INFO  @ Tue, 17 May 2016 09:46:07:  20000000 
INFO  @ Tue, 17 May 2016 09:46:09:  21000000 
INFO  @ Tue, 17 May 2016 09:46:11:  22000000 
INFO  @ Tue, 17 May 2016 09:46:13:  23000000 
INFO  @ Tue, 17 May 2016 09:46:15:  24000000 
INFO  @ Tue, 17 May 2016 09:46:17:  25000000 
INFO  @ Tue, 17 May 2016 09:46:19:  26000000 
INFO  @ Tue, 17 May 2016 09:46:21:  27000000 
INFO  @ Tue, 17 May 2016 09:46:24: #1 tag size is determined as 56 bps 
INFO  @ Tue, 17 May 2016 09:46:24: #1 tag size = 56 
INFO  @ Tue, 17 May 2016 09:46:24: #1  total tags in treatment: 27028176 
INFO  @ Tue, 17 May 2016 09:46:24: #1 finished! 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:46:24: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:46:24: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 09:46:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:47:40: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:49:39: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 09:49:44: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 09:49:47: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 09:49:49: Done! 
INFO  @ Tue, 17 May 2016 09:50:01: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 09:50:01: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:50:01: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:50:03:  1000000 
INFO  @ Tue, 17 May 2016 09:50:05:  2000000 
INFO  @ Tue, 17 May 2016 09:50:07:  3000000 
INFO  @ Tue, 17 May 2016 09:50:09:  4000000 
INFO  @ Tue, 17 May 2016 09:50:11:  5000000 
INFO  @ Tue, 17 May 2016 09:50:13:  6000000 
INFO  @ Tue, 17 May 2016 09:50:15:  7000000 
INFO  @ Tue, 17 May 2016 09:50:17:  8000000 
INFO  @ Tue, 17 May 2016 09:50:19:  9000000 
INFO  @ Tue, 17 May 2016 09:50:21:  10000000 
INFO  @ Tue, 17 May 2016 09:50:23:  11000000 
INFO  @ Tue, 17 May 2016 09:50:26:  12000000 
INFO  @ Tue, 17 May 2016 09:50:28:  13000000 
INFO  @ Tue, 17 May 2016 09:50:30:  14000000 
INFO  @ Tue, 17 May 2016 09:50:32:  15000000 
INFO  @ Tue, 17 May 2016 09:50:34:  16000000 
INFO  @ Tue, 17 May 2016 09:50:36:  17000000 
INFO  @ Tue, 17 May 2016 09:50:38:  18000000 
INFO  @ Tue, 17 May 2016 09:50:40:  19000000 
INFO  @ Tue, 17 May 2016 09:50:42:  20000000 
INFO  @ Tue, 17 May 2016 09:50:44:  21000000 
INFO  @ Tue, 17 May 2016 09:50:46:  22000000 
INFO  @ Tue, 17 May 2016 09:50:48:  23000000 
INFO  @ Tue, 17 May 2016 09:50:51:  24000000 
INFO  @ Tue, 17 May 2016 09:50:53:  25000000 
INFO  @ Tue, 17 May 2016 09:50:55:  26000000 
INFO  @ Tue, 17 May 2016 09:50:57:  27000000 
INFO  @ Tue, 17 May 2016 09:50:59: #1 tag size is determined as 56 bps 
INFO  @ Tue, 17 May 2016 09:50:59: #1 tag size = 56 
INFO  @ Tue, 17 May 2016 09:50:59: #1  total tags in treatment: 27028176 
INFO  @ Tue, 17 May 2016 09:50:59: #1 finished! 
INFO  @ Tue, 17 May 2016 09:50:59: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:50:59: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:50:59: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:50:59: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:50:59: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:50:59: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 09:50:59: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 09:50:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:52:16: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 09:52:16: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 09:52:16: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 09:52:16: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 09:52:16: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:00:00: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 10:00:08: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 10:00:15: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 10:00:18: 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	23639

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

Start	2016-05-17 09:45:22
End	2016-05-17 10:00:33
Elapsed	00:15:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 09:45:26: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 09:45:26: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:45:26: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:45:29:  1000000 
INFO  @ Tue, 17 May 2016 09:45:31:  2000000 
INFO  @ Tue, 17 May 2016 09:45:33:  3000000 
INFO  @ Tue, 17 May 2016 09:45:35:  4000000 
INFO  @ Tue, 17 May 2016 09:45:37:  5000000 
INFO  @ Tue, 17 May 2016 09:45:39:  6000000 
INFO  @ Tue, 17 May 2016 09:45:41:  7000000 
INFO  @ Tue, 17 May 2016 09:45:43:  8000000 
INFO  @ Tue, 17 May 2016 09:45:45:  9000000 
INFO  @ Tue, 17 May 2016 09:45:47:  10000000 
INFO  @ Tue, 17 May 2016 09:45:49:  11000000 
INFO  @ Tue, 17 May 2016 09:45:51:  12000000 
INFO  @ Tue, 17 May 2016 09:45:53:  13000000 
INFO  @ Tue, 17 May 2016 09:45:55:  14000000 
INFO  @ Tue, 17 May 2016 09:45:57:  15000000 
INFO  @ Tue, 17 May 2016 09:45:59:  16000000 
INFO  @ Tue, 17 May 2016 09:46:01:  17000000 
INFO  @ Tue, 17 May 2016 09:46:03:  18000000 
INFO  @ Tue, 17 May 2016 09:46:05:  19000000 
INFO  @ Tue, 17 May 2016 09:46:07:  20000000 
INFO  @ Tue, 17 May 2016 09:46:09:  21000000 
INFO  @ Tue, 17 May 2016 09:46:12:  22000000 
INFO  @ Tue, 17 May 2016 09:46:14:  23000000 
INFO  @ Tue, 17 May 2016 09:46:16:  24000000 
INFO  @ Tue, 17 May 2016 09:46:18:  25000000 
INFO  @ Tue, 17 May 2016 09:46:20:  26000000 
INFO  @ Tue, 17 May 2016 09:46:22:  27000000 
INFO  @ Tue, 17 May 2016 09:46:24: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 09:46:24: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 09:46:24: #1  total tags in treatment: 27028176 
INFO  @ Tue, 17 May 2016 09:46:24: #1 finished! 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:46:24: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:46:24: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:46:24: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 09:46:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:47:42: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:49:47: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 09:49:52: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 09:49:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 09:49:57: Done! 
INFO  @ Tue, 17 May 2016 09:50:08: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 09:50:08: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:50:08: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:50:10:  1000000 
INFO  @ Tue, 17 May 2016 09:50:12:  2000000 
INFO  @ Tue, 17 May 2016 09:50:14:  3000000 
INFO  @ Tue, 17 May 2016 09:50:16:  4000000 
INFO  @ Tue, 17 May 2016 09:50:18:  5000000 
INFO  @ Tue, 17 May 2016 09:50:21:  6000000 
INFO  @ Tue, 17 May 2016 09:50:23:  7000000 
INFO  @ Tue, 17 May 2016 09:50:25:  8000000 
INFO  @ Tue, 17 May 2016 09:50:27:  9000000 
INFO  @ Tue, 17 May 2016 09:50:29:  10000000 
INFO  @ Tue, 17 May 2016 09:50:31:  11000000 
INFO  @ Tue, 17 May 2016 09:50:33:  12000000 
INFO  @ Tue, 17 May 2016 09:50:35:  13000000 
INFO  @ Tue, 17 May 2016 09:50:37:  14000000 
INFO  @ Tue, 17 May 2016 09:50:39:  15000000 
INFO  @ Tue, 17 May 2016 09:50:41:  16000000 
INFO  @ Tue, 17 May 2016 09:50:43:  17000000 
INFO  @ Tue, 17 May 2016 09:50:45:  18000000 
INFO  @ Tue, 17 May 2016 09:50:47:  19000000 
INFO  @ Tue, 17 May 2016 09:50:49:  20000000 
INFO  @ Tue, 17 May 2016 09:50:51:  21000000 
INFO  @ Tue, 17 May 2016 09:50:53:  22000000 
INFO  @ Tue, 17 May 2016 09:50:55:  23000000 
INFO  @ Tue, 17 May 2016 09:50:58:  24000000 
INFO  @ Tue, 17 May 2016 09:51:00:  25000000 
INFO  @ Tue, 17 May 2016 09:51:02:  26000000 
INFO  @ Tue, 17 May 2016 09:51:04:  27000000 
INFO  @ Tue, 17 May 2016 09:51:06: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 09:51:06: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 09:51:06: #1  total tags in treatment: 27028176 
INFO  @ Tue, 17 May 2016 09:51:06: #1 finished! 
INFO  @ Tue, 17 May 2016 09:51:06: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:51:06: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:51:06: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:51:06: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:51:06: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:51:06: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 09:51:06: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 09:51:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:52:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 09:52:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 09:52:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 09:52:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 09:52:24: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:00:14: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 10:00:20: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 10:00:25: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 10:00:27: 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	29875

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

Start	2016-05-17 10:00:34
End	2016-05-17 10:21:46
Elapsed	00:21:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 10:00:37: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 10:00:37: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:00:37: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:00:39:  1000000 
INFO  @ Tue, 17 May 2016 10:00:41:  2000000 
INFO  @ Tue, 17 May 2016 10:00:43:  3000000 
INFO  @ Tue, 17 May 2016 10:00:45:  4000000 
INFO  @ Tue, 17 May 2016 10:00:47:  5000000 
INFO  @ Tue, 17 May 2016 10:00:49:  6000000 
INFO  @ Tue, 17 May 2016 10:00:51:  7000000 
INFO  @ Tue, 17 May 2016 10:00:53:  8000000 
INFO  @ Tue, 17 May 2016 10:00:55:  9000000 
INFO  @ Tue, 17 May 2016 10:00:57:  10000000 
INFO  @ Tue, 17 May 2016 10:00:59:  11000000 
INFO  @ Tue, 17 May 2016 10:01:01:  12000000 
INFO  @ Tue, 17 May 2016 10:01:03:  13000000 
INFO  @ Tue, 17 May 2016 10:01:05:  14000000 
INFO  @ Tue, 17 May 2016 10:01:07:  15000000 
INFO  @ Tue, 17 May 2016 10:01:09:  16000000 
INFO  @ Tue, 17 May 2016 10:01:11:  17000000 
INFO  @ Tue, 17 May 2016 10:01:13:  18000000 
INFO  @ Tue, 17 May 2016 10:01:15:  19000000 
INFO  @ Tue, 17 May 2016 10:01:17:  20000000 
INFO  @ Tue, 17 May 2016 10:01:19:  21000000 
INFO  @ Tue, 17 May 2016 10:01:21:  22000000 
INFO  @ Tue, 17 May 2016 10:01:23:  23000000 
INFO  @ Tue, 17 May 2016 10:01:25:  24000000 
INFO  @ Tue, 17 May 2016 10:01:27:  25000000 
INFO  @ Tue, 17 May 2016 10:01:29:  26000000 
INFO  @ Tue, 17 May 2016 10:01:31:  27000000 
INFO  @ Tue, 17 May 2016 10:01:33:  28000000 
INFO  @ Tue, 17 May 2016 10:01:35:  29000000 
INFO  @ Tue, 17 May 2016 10:01:37:  30000000 
INFO  @ Tue, 17 May 2016 10:01:39:  31000000 
INFO  @ Tue, 17 May 2016 10:01:41:  32000000 
INFO  @ Tue, 17 May 2016 10:01:43:  33000000 
INFO  @ Tue, 17 May 2016 10:01:45:  34000000 
INFO  @ Tue, 17 May 2016 10:01:47:  35000000 
INFO  @ Tue, 17 May 2016 10:01:49:  36000000 
INFO  @ Tue, 17 May 2016 10:01:51:  37000000 
INFO  @ Tue, 17 May 2016 10:01:53:  38000000 
INFO  @ Tue, 17 May 2016 10:01:55:  39000000 
INFO  @ Tue, 17 May 2016 10:01:57:  40000000 
INFO  @ Tue, 17 May 2016 10:01:59:  41000000 
INFO  @ Tue, 17 May 2016 10:02:01:  42000000 
INFO  @ Tue, 17 May 2016 10:02:03:  43000000 
INFO  @ Tue, 17 May 2016 10:02:05:  44000000 
INFO  @ Tue, 17 May 2016 10:02:07:  45000000 
INFO  @ Tue, 17 May 2016 10:02:09:  46000000 
INFO  @ Tue, 17 May 2016 10:02:11:  47000000 
INFO  @ Tue, 17 May 2016 10:02:13:  48000000 
INFO  @ Tue, 17 May 2016 10:02:15:  49000000 
INFO  @ Tue, 17 May 2016 10:02:17:  50000000 
INFO  @ Tue, 17 May 2016 10:02:23: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 10:02:23: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 10:02:23: #1  total tags in treatment: 50542262 
INFO  @ Tue, 17 May 2016 10:02:23: #1 finished! 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:02:23: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:02:23: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 10:02:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:04:22: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:07:26: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 10:07:31: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 10:07:34: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 10:07:36: Done! 
INFO  @ Tue, 17 May 2016 10:07:46: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 10:07:46: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:07:46: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:07:48:  1000000 
INFO  @ Tue, 17 May 2016 10:07:50:  2000000 
INFO  @ Tue, 17 May 2016 10:07:52:  3000000 
INFO  @ Tue, 17 May 2016 10:07:54:  4000000 
INFO  @ Tue, 17 May 2016 10:07:56:  5000000 
INFO  @ Tue, 17 May 2016 10:07:58:  6000000 
INFO  @ Tue, 17 May 2016 10:08:00:  7000000 
INFO  @ Tue, 17 May 2016 10:08:02:  8000000 
INFO  @ Tue, 17 May 2016 10:08:04:  9000000 
INFO  @ Tue, 17 May 2016 10:08:06:  10000000 
INFO  @ Tue, 17 May 2016 10:08:08:  11000000 
INFO  @ Tue, 17 May 2016 10:08:10:  12000000 
INFO  @ Tue, 17 May 2016 10:08:12:  13000000 
INFO  @ Tue, 17 May 2016 10:08:14:  14000000 
INFO  @ Tue, 17 May 2016 10:08:16:  15000000 
INFO  @ Tue, 17 May 2016 10:08:18:  16000000 
INFO  @ Tue, 17 May 2016 10:08:20:  17000000 
INFO  @ Tue, 17 May 2016 10:08:22:  18000000 
INFO  @ Tue, 17 May 2016 10:08:24:  19000000 
INFO  @ Tue, 17 May 2016 10:08:26:  20000000 
INFO  @ Tue, 17 May 2016 10:08:28:  21000000 
INFO  @ Tue, 17 May 2016 10:08:30:  22000000 
INFO  @ Tue, 17 May 2016 10:08:32:  23000000 
INFO  @ Tue, 17 May 2016 10:08:34:  24000000 
INFO  @ Tue, 17 May 2016 10:08:36:  25000000 
INFO  @ Tue, 17 May 2016 10:08:38:  26000000 
INFO  @ Tue, 17 May 2016 10:08:40:  27000000 
INFO  @ Tue, 17 May 2016 10:08:42:  28000000 
INFO  @ Tue, 17 May 2016 10:08:44:  29000000 
INFO  @ Tue, 17 May 2016 10:08:46:  30000000 
INFO  @ Tue, 17 May 2016 10:08:48:  31000000 
INFO  @ Tue, 17 May 2016 10:08:50:  32000000 
INFO  @ Tue, 17 May 2016 10:08:52:  33000000 
INFO  @ Tue, 17 May 2016 10:08:54:  34000000 
INFO  @ Tue, 17 May 2016 10:08:55:  35000000 
INFO  @ Tue, 17 May 2016 10:08:57:  36000000 
INFO  @ Tue, 17 May 2016 10:08:59:  37000000 
INFO  @ Tue, 17 May 2016 10:09:01:  38000000 
INFO  @ Tue, 17 May 2016 10:09:03:  39000000 
INFO  @ Tue, 17 May 2016 10:09:05:  40000000 
INFO  @ Tue, 17 May 2016 10:09:07:  41000000 
INFO  @ Tue, 17 May 2016 10:09:09:  42000000 
INFO  @ Tue, 17 May 2016 10:09:11:  43000000 
INFO  @ Tue, 17 May 2016 10:09:13:  44000000 
INFO  @ Tue, 17 May 2016 10:09:15:  45000000 
INFO  @ Tue, 17 May 2016 10:09:17:  46000000 
INFO  @ Tue, 17 May 2016 10:09:19:  47000000 
INFO  @ Tue, 17 May 2016 10:09:21:  48000000 
INFO  @ Tue, 17 May 2016 10:09:23:  49000000 
INFO  @ Tue, 17 May 2016 10:09:25:  50000000 
INFO  @ Tue, 17 May 2016 10:09:30: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 10:09:30: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 10:09:30: #1  total tags in treatment: 50542262 
INFO  @ Tue, 17 May 2016 10:09:30: #1 finished! 
INFO  @ Tue, 17 May 2016 10:09:30: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:09:30: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:09:30: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:09:30: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:09:30: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:09:30: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 10:09:30: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 10:09:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:11:29: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 10:11:29: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 10:11:29: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 10:11:29: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 10:11:29: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:21:28: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 10:21:33: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 10:21:37: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 10:21:40: Done!

Num	17
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_22
Name	macs2_atac rep1
Thread	thread_20
PID	29880

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

Start	2016-05-17 10:00:34
End	2016-05-17 11:01:25
Elapsed	01:00:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 10:00:37: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 10:00:37: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:00:37: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:00:39:  1000000 
INFO  @ Tue, 17 May 2016 10:00:41:  2000000 
INFO  @ Tue, 17 May 2016 10:00:43:  3000000 
INFO  @ Tue, 17 May 2016 10:00:45:  4000000 
INFO  @ Tue, 17 May 2016 10:00:47:  5000000 
INFO  @ Tue, 17 May 2016 10:00:49:  6000000 
INFO  @ Tue, 17 May 2016 10:00:51:  7000000 
INFO  @ Tue, 17 May 2016 10:00:53:  8000000 
INFO  @ Tue, 17 May 2016 10:00:55:  9000000 
INFO  @ Tue, 17 May 2016 10:00:57:  10000000 
INFO  @ Tue, 17 May 2016 10:00:59:  11000000 
INFO  @ Tue, 17 May 2016 10:01:01:  12000000 
INFO  @ Tue, 17 May 2016 10:01:03:  13000000 
INFO  @ Tue, 17 May 2016 10:01:05:  14000000 
INFO  @ Tue, 17 May 2016 10:01:07:  15000000 
INFO  @ Tue, 17 May 2016 10:01:09:  16000000 
INFO  @ Tue, 17 May 2016 10:01:11:  17000000 
INFO  @ Tue, 17 May 2016 10:01:13:  18000000 
INFO  @ Tue, 17 May 2016 10:01:15:  19000000 
INFO  @ Tue, 17 May 2016 10:01:17:  20000000 
INFO  @ Tue, 17 May 2016 10:01:19:  21000000 
INFO  @ Tue, 17 May 2016 10:01:21:  22000000 
INFO  @ Tue, 17 May 2016 10:01:23:  23000000 
INFO  @ Tue, 17 May 2016 10:01:25:  24000000 
INFO  @ Tue, 17 May 2016 10:01:27:  25000000 
INFO  @ Tue, 17 May 2016 10:01:29:  26000000 
INFO  @ Tue, 17 May 2016 10:01:31:  27000000 
INFO  @ Tue, 17 May 2016 10:01:33:  28000000 
INFO  @ Tue, 17 May 2016 10:01:35:  29000000 
INFO  @ Tue, 17 May 2016 10:01:37:  30000000 
INFO  @ Tue, 17 May 2016 10:01:39:  31000000 
INFO  @ Tue, 17 May 2016 10:01:41:  32000000 
INFO  @ Tue, 17 May 2016 10:01:43:  33000000 
INFO  @ Tue, 17 May 2016 10:01:45:  34000000 
INFO  @ Tue, 17 May 2016 10:01:47:  35000000 
INFO  @ Tue, 17 May 2016 10:01:49:  36000000 
INFO  @ Tue, 17 May 2016 10:01:51:  37000000 
INFO  @ Tue, 17 May 2016 10:01:53:  38000000 
INFO  @ Tue, 17 May 2016 10:01:55:  39000000 
INFO  @ Tue, 17 May 2016 10:01:57:  40000000 
INFO  @ Tue, 17 May 2016 10:01:59:  41000000 
INFO  @ Tue, 17 May 2016 10:02:01:  42000000 
INFO  @ Tue, 17 May 2016 10:02:03:  43000000 
INFO  @ Tue, 17 May 2016 10:02:05:  44000000 
INFO  @ Tue, 17 May 2016 10:02:08:  45000000 
INFO  @ Tue, 17 May 2016 10:02:10:  46000000 
INFO  @ Tue, 17 May 2016 10:02:12:  47000000 
INFO  @ Tue, 17 May 2016 10:02:14:  48000000 
INFO  @ Tue, 17 May 2016 10:02:16:  49000000 
INFO  @ Tue, 17 May 2016 10:02:18:  50000000 
INFO  @ Tue, 17 May 2016 10:02:23: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 10:02:23: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 10:02:23: #1  total tags in treatment: 50542262 
INFO  @ Tue, 17 May 2016 10:02:23: #1 finished! 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:02:23: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:02:23: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:02:23: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 10:02:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:04:26: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:07:07: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 10:07:11: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 10:07:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 10:07:16: Done! 
INFO  @ Tue, 17 May 2016 10:07:26: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 10:07:26: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:07:26: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:07:29:  1000000 
INFO  @ Tue, 17 May 2016 10:07:31:  2000000 
INFO  @ Tue, 17 May 2016 10:07:33:  3000000 
INFO  @ Tue, 17 May 2016 10:07:35:  4000000 
INFO  @ Tue, 17 May 2016 10:07:37:  5000000 
INFO  @ Tue, 17 May 2016 10:07:39:  6000000 
INFO  @ Tue, 17 May 2016 10:07:41:  7000000 
INFO  @ Tue, 17 May 2016 10:07:43:  8000000 
INFO  @ Tue, 17 May 2016 10:07:46:  9000000 
INFO  @ Tue, 17 May 2016 10:07:48:  10000000 
INFO  @ Tue, 17 May 2016 10:07:50:  11000000 
INFO  @ Tue, 17 May 2016 10:07:52:  12000000 
INFO  @ Tue, 17 May 2016 10:07:54:  13000000 
INFO  @ Tue, 17 May 2016 10:07:56:  14000000 
INFO  @ Tue, 17 May 2016 10:07:58:  15000000 
INFO  @ Tue, 17 May 2016 10:08:01:  16000000 
INFO  @ Tue, 17 May 2016 10:08:03:  17000000 
INFO  @ Tue, 17 May 2016 10:08:05:  18000000 
INFO  @ Tue, 17 May 2016 10:08:07:  19000000 
INFO  @ Tue, 17 May 2016 10:08:09:  20000000 
INFO  @ Tue, 17 May 2016 10:08:11:  21000000 
INFO  @ Tue, 17 May 2016 10:08:13:  22000000 
INFO  @ Tue, 17 May 2016 10:08:16:  23000000 
INFO  @ Tue, 17 May 2016 10:08:18:  24000000 
INFO  @ Tue, 17 May 2016 10:08:20:  25000000 
INFO  @ Tue, 17 May 2016 10:08:22:  26000000 
INFO  @ Tue, 17 May 2016 10:08:24:  27000000 
INFO  @ Tue, 17 May 2016 10:08:26:  28000000 
INFO  @ Tue, 17 May 2016 10:08:29:  29000000 
INFO  @ Tue, 17 May 2016 10:08:31:  30000000 
INFO  @ Tue, 17 May 2016 10:08:33:  31000000 
INFO  @ Tue, 17 May 2016 10:08:35:  32000000 
INFO  @ Tue, 17 May 2016 10:08:37:  33000000 
INFO  @ Tue, 17 May 2016 10:08:39:  34000000 
INFO  @ Tue, 17 May 2016 10:08:41:  35000000 
INFO  @ Tue, 17 May 2016 10:08:44:  36000000 
INFO  @ Tue, 17 May 2016 10:08:46:  37000000 
INFO  @ Tue, 17 May 2016 10:08:48:  38000000 
INFO  @ Tue, 17 May 2016 10:08:50:  39000000 
INFO  @ Tue, 17 May 2016 10:08:52:  40000000 
INFO  @ Tue, 17 May 2016 10:08:54:  41000000 
INFO  @ Tue, 17 May 2016 10:08:56:  42000000 
INFO  @ Tue, 17 May 2016 10:08:59:  43000000 
INFO  @ Tue, 17 May 2016 10:09:01:  44000000 
INFO  @ Tue, 17 May 2016 10:09:03:  45000000 
INFO  @ Tue, 17 May 2016 10:09:05:  46000000 
INFO  @ Tue, 17 May 2016 10:09:07:  47000000 
INFO  @ Tue, 17 May 2016 10:09:09:  48000000 
INFO  @ Tue, 17 May 2016 10:09:11:  49000000 
INFO  @ Tue, 17 May 2016 10:09:13:  50000000 
INFO  @ Tue, 17 May 2016 10:09:19: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 10:09:19: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 10:09:19: #1  total tags in treatment: 50542262 
INFO  @ Tue, 17 May 2016 10:09:19: #1 finished! 
INFO  @ Tue, 17 May 2016 10:09:19: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:09:19: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:09:19: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:09:19: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:09:19: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:09:19: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 10:09:19: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 10:09:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:11:17: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 10:11:17: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 10:11:17: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 10:11:17: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 10:11:17: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:19:16: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 10:19:20: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 10:19:22: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 10:19:24: Done! 
INFO  @ Tue, 17 May 2016 10:19:28: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 10:21:26: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 10:22:05: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 10:23:03: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 10:28:48: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 10:32:09: Finished 'FE'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 10:43:49: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 10:45:42: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 10:46:20: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 10:46:59: Values in your input bedGraph files will be multiplied by 50.542262 ... 
INFO  @ Tue, 17 May 2016 10:51:54: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 10:52:36: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 10:54:59: Finished 'ppois'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	12230

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

Start	2016-05-17 13:54:05
End	2016-05-17 14:15:42
Elapsed	00:21:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	20536

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

Start	2016-05-17 14:15:43
End	2016-05-17 14:18:07
Elapsed	00:02:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	20760

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

Start	2016-05-17 14:18:09
End	2016-05-17 14:20:31
Elapsed	00:02:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	22297

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

Start	2016-05-17 14:20:32
End	2016-05-17 14:22:32
Elapsed	00:01:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.00" | \
			gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.01" | \
			gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22458

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

Start	2016-05-17 14:22:32
End	2016-05-17 14:23:52
Elapsed	00:01:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22463

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

Start	2016-05-17 14:22:33
End	2016-05-17 14:23:16
Elapsed	00:00:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22471

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

Start	2016-05-17 14:22:33
End	2016-05-17 14:23:18
Elapsed	00:00:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22647

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

Start	2016-05-17 14:23:53
End	2016-05-17 14:24:56
Elapsed	00:01:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	22756

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

Start	2016-05-17 14:24:56
End	2016-05-17 14:54:42
Elapsed	00:29:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmpj22d1c/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign59881011b2cd
done. read 20270611 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1242691 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.229477341750141 
Top 3 estimates for fragment length 0 
Window half size 490 
Phantom peak location 80 
Phantom peak Correlation 0.2504782 
Normalized Strand cross-correlation coefficient (NSC) 1.846616 
Relative Strand Cross correlation Coefficient (RSC) 0.8336026 
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	22758

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

Start	2016-05-17 14:24:57
End	2016-05-17 14:36:04
Elapsed	00:11:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:24:59: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:24:59: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:24:59: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:25:01:  1000000 
INFO  @ Tue, 17 May 2016 14:25:03:  2000000 
INFO  @ Tue, 17 May 2016 14:25:05:  3000000 
INFO  @ Tue, 17 May 2016 14:25:07:  4000000 
INFO  @ Tue, 17 May 2016 14:25:09:  5000000 
INFO  @ Tue, 17 May 2016 14:25:11:  6000000 
INFO  @ Tue, 17 May 2016 14:25:13:  7000000 
INFO  @ Tue, 17 May 2016 14:25:15:  8000000 
INFO  @ Tue, 17 May 2016 14:25:17:  9000000 
INFO  @ Tue, 17 May 2016 14:25:19:  10000000 
INFO  @ Tue, 17 May 2016 14:25:20:  11000000 
INFO  @ Tue, 17 May 2016 14:25:22:  12000000 
INFO  @ Tue, 17 May 2016 14:25:24:  13000000 
INFO  @ Tue, 17 May 2016 14:25:26:  14000000 
INFO  @ Tue, 17 May 2016 14:25:28:  15000000 
INFO  @ Tue, 17 May 2016 14:25:30:  16000000 
INFO  @ Tue, 17 May 2016 14:25:32:  17000000 
INFO  @ Tue, 17 May 2016 14:25:34:  18000000 
INFO  @ Tue, 17 May 2016 14:25:36:  19000000 
INFO  @ Tue, 17 May 2016 14:25:38:  20000000 
INFO  @ Tue, 17 May 2016 14:25:40:  21000000 
INFO  @ Tue, 17 May 2016 14:25:42:  22000000 
INFO  @ Tue, 17 May 2016 14:25:45: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 14:25:45: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 14:25:45: #1  total tags in treatment: 22479980 
INFO  @ Tue, 17 May 2016 14:25:45: #1 finished! 
INFO  @ Tue, 17 May 2016 14:25:45: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:25:45: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:25:45: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:25:45: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:25:45: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:25:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 14:25:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:26:52: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:28:20: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 14:28:23: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 14:28:25: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 14:28:27: Done! 
INFO  @ Tue, 17 May 2016 14:28:36: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:28:36: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:28:36: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:28:38:  1000000 
INFO  @ Tue, 17 May 2016 14:28:40:  2000000 
INFO  @ Tue, 17 May 2016 14:28:42:  3000000 
INFO  @ Tue, 17 May 2016 14:28:44:  4000000 
INFO  @ Tue, 17 May 2016 14:28:46:  5000000 
INFO  @ Tue, 17 May 2016 14:28:48:  6000000 
INFO  @ Tue, 17 May 2016 14:28:50:  7000000 
INFO  @ Tue, 17 May 2016 14:28:52:  8000000 
INFO  @ Tue, 17 May 2016 14:28:53:  9000000 
INFO  @ Tue, 17 May 2016 14:28:55:  10000000 
INFO  @ Tue, 17 May 2016 14:28:57:  11000000 
INFO  @ Tue, 17 May 2016 14:28:59:  12000000 
INFO  @ Tue, 17 May 2016 14:29:01:  13000000 
INFO  @ Tue, 17 May 2016 14:29:03:  14000000 
INFO  @ Tue, 17 May 2016 14:29:05:  15000000 
INFO  @ Tue, 17 May 2016 14:29:07:  16000000 
INFO  @ Tue, 17 May 2016 14:29:08:  17000000 
INFO  @ Tue, 17 May 2016 14:29:10:  18000000 
INFO  @ Tue, 17 May 2016 14:29:12:  19000000 
INFO  @ Tue, 17 May 2016 14:29:14:  20000000 
INFO  @ Tue, 17 May 2016 14:29:16:  21000000 
INFO  @ Tue, 17 May 2016 14:29:18:  22000000 
INFO  @ Tue, 17 May 2016 14:29:20: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 14:29:20: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 14:29:20: #1  total tags in treatment: 22479980 
INFO  @ Tue, 17 May 2016 14:29:20: #1 finished! 
INFO  @ Tue, 17 May 2016 14:29:20: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:29:20: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:29:20: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:29:20: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:29:20: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:29:20: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 14:29:20: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 14:29:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:30:27: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 14:30:27: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 14:30:27: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 14:30:27: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 14:30:27: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:35:51: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 14:35:56: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 14:35:59: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 14:36:01: 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	22768

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

Start	2016-05-17 14:24:57
End	2016-05-17 14:36:11
Elapsed	00:11:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:24:59: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:24:59: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:24:59: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:25:01:  1000000 
INFO  @ Tue, 17 May 2016 14:25:03:  2000000 
INFO  @ Tue, 17 May 2016 14:25:05:  3000000 
INFO  @ Tue, 17 May 2016 14:25:07:  4000000 
INFO  @ Tue, 17 May 2016 14:25:09:  5000000 
INFO  @ Tue, 17 May 2016 14:25:11:  6000000 
INFO  @ Tue, 17 May 2016 14:25:13:  7000000 
INFO  @ Tue, 17 May 2016 14:25:15:  8000000 
INFO  @ Tue, 17 May 2016 14:25:16:  9000000 
INFO  @ Tue, 17 May 2016 14:25:18:  10000000 
INFO  @ Tue, 17 May 2016 14:25:20:  11000000 
INFO  @ Tue, 17 May 2016 14:25:22:  12000000 
INFO  @ Tue, 17 May 2016 14:25:24:  13000000 
INFO  @ Tue, 17 May 2016 14:25:26:  14000000 
INFO  @ Tue, 17 May 2016 14:25:28:  15000000 
INFO  @ Tue, 17 May 2016 14:25:30:  16000000 
INFO  @ Tue, 17 May 2016 14:25:32:  17000000 
INFO  @ Tue, 17 May 2016 14:25:34:  18000000 
INFO  @ Tue, 17 May 2016 14:25:36:  19000000 
INFO  @ Tue, 17 May 2016 14:25:38:  20000000 
INFO  @ Tue, 17 May 2016 14:25:39:  21000000 
INFO  @ Tue, 17 May 2016 14:25:41:  22000000 
INFO  @ Tue, 17 May 2016 14:25:44: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 14:25:44: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 14:25:44: #1  total tags in treatment: 22479980 
INFO  @ Tue, 17 May 2016 14:25:44: #1 finished! 
INFO  @ Tue, 17 May 2016 14:25:44: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:25:44: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:25:44: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:25:44: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:25:44: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:25:44: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 14:25:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:26:50: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:28:20: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 14:28:23: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 14:28:25: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 14:28:27: Done! 
INFO  @ Tue, 17 May 2016 14:28:37: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:28:37: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:28:37: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:28:39:  1000000 
INFO  @ Tue, 17 May 2016 14:28:41:  2000000 
INFO  @ Tue, 17 May 2016 14:28:43:  3000000 
INFO  @ Tue, 17 May 2016 14:28:45:  4000000 
INFO  @ Tue, 17 May 2016 14:28:47:  5000000 
INFO  @ Tue, 17 May 2016 14:28:49:  6000000 
INFO  @ Tue, 17 May 2016 14:28:51:  7000000 
INFO  @ Tue, 17 May 2016 14:28:53:  8000000 
INFO  @ Tue, 17 May 2016 14:28:55:  9000000 
INFO  @ Tue, 17 May 2016 14:28:57:  10000000 
INFO  @ Tue, 17 May 2016 14:28:59:  11000000 
INFO  @ Tue, 17 May 2016 14:29:01:  12000000 
INFO  @ Tue, 17 May 2016 14:29:03:  13000000 
INFO  @ Tue, 17 May 2016 14:29:05:  14000000 
INFO  @ Tue, 17 May 2016 14:29:07:  15000000 
INFO  @ Tue, 17 May 2016 14:29:09:  16000000 
INFO  @ Tue, 17 May 2016 14:29:11:  17000000 
INFO  @ Tue, 17 May 2016 14:29:13:  18000000 
INFO  @ Tue, 17 May 2016 14:29:15:  19000000 
INFO  @ Tue, 17 May 2016 14:29:17:  20000000 
INFO  @ Tue, 17 May 2016 14:29:19:  21000000 
INFO  @ Tue, 17 May 2016 14:29:21:  22000000 
INFO  @ Tue, 17 May 2016 14:29:23: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 14:29:23: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 14:29:23: #1  total tags in treatment: 22479980 
INFO  @ Tue, 17 May 2016 14:29:23: #1 finished! 
INFO  @ Tue, 17 May 2016 14:29:23: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:29:23: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:29:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:29:23: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:29:23: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:29:23: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 14:29:23: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 14:29:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:30:30: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 14:30:30: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 14:30:30: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 14:30:30: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 14:30:30: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:35:56: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 14:36:02: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 14:36:05: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 14:36:07: 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	27899

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

Start	2016-05-17 14:36:12
End	2016-05-17 14:54:21
Elapsed	00:18:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:36:14: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:36:14: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:36:14: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:36:16:  1000000 
INFO  @ Tue, 17 May 2016 14:36:18:  2000000 
INFO  @ Tue, 17 May 2016 14:36:20:  3000000 
INFO  @ Tue, 17 May 2016 14:36:22:  4000000 
INFO  @ Tue, 17 May 2016 14:36:24:  5000000 
INFO  @ Tue, 17 May 2016 14:36:26:  6000000 
INFO  @ Tue, 17 May 2016 14:36:28:  7000000 
INFO  @ Tue, 17 May 2016 14:36:30:  8000000 
INFO  @ Tue, 17 May 2016 14:36:32:  9000000 
INFO  @ Tue, 17 May 2016 14:36:34:  10000000 
INFO  @ Tue, 17 May 2016 14:36:36:  11000000 
INFO  @ Tue, 17 May 2016 14:36:38:  12000000 
INFO  @ Tue, 17 May 2016 14:36:41:  13000000 
INFO  @ Tue, 17 May 2016 14:36:43:  14000000 
INFO  @ Tue, 17 May 2016 14:36:45:  15000000 
INFO  @ Tue, 17 May 2016 14:36:47:  16000000 
INFO  @ Tue, 17 May 2016 14:36:49:  17000000 
INFO  @ Tue, 17 May 2016 14:36:51:  18000000 
INFO  @ Tue, 17 May 2016 14:36:53:  19000000 
INFO  @ Tue, 17 May 2016 14:36:55:  20000000 
INFO  @ Tue, 17 May 2016 14:36:57:  21000000 
INFO  @ Tue, 17 May 2016 14:36:59:  22000000 
INFO  @ Tue, 17 May 2016 14:37:01:  23000000 
INFO  @ Tue, 17 May 2016 14:37:03:  24000000 
INFO  @ Tue, 17 May 2016 14:37:05:  25000000 
INFO  @ Tue, 17 May 2016 14:37:07:  26000000 
INFO  @ Tue, 17 May 2016 14:37:09:  27000000 
INFO  @ Tue, 17 May 2016 14:37:11:  28000000 
INFO  @ Tue, 17 May 2016 14:37:13:  29000000 
INFO  @ Tue, 17 May 2016 14:37:15:  30000000 
INFO  @ Tue, 17 May 2016 14:37:17:  31000000 
INFO  @ Tue, 17 May 2016 14:37:19:  32000000 
INFO  @ Tue, 17 May 2016 14:37:21:  33000000 
INFO  @ Tue, 17 May 2016 14:37:23:  34000000 
INFO  @ Tue, 17 May 2016 14:37:25:  35000000 
INFO  @ Tue, 17 May 2016 14:37:27:  36000000 
INFO  @ Tue, 17 May 2016 14:37:29:  37000000 
INFO  @ Tue, 17 May 2016 14:37:31:  38000000 
INFO  @ Tue, 17 May 2016 14:37:33:  39000000 
INFO  @ Tue, 17 May 2016 14:37:35:  40000000 
INFO  @ Tue, 17 May 2016 14:37:39: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 14:37:39: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 14:37:39: #1  total tags in treatment: 40541222 
INFO  @ Tue, 17 May 2016 14:37:39: #1 finished! 
INFO  @ Tue, 17 May 2016 14:37:39: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:37:39: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:37:39: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:37:39: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:37:39: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:37:39: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 14:37:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:39:18: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:42:19: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 14:42:23: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 14:42:25: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 14:42:27: Done! 
INFO  @ Tue, 17 May 2016 14:42:37: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:42:37: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:42:37: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:42:39:  1000000 
INFO  @ Tue, 17 May 2016 14:42:41:  2000000 
INFO  @ Tue, 17 May 2016 14:42:43:  3000000 
INFO  @ Tue, 17 May 2016 14:42:45:  4000000 
INFO  @ Tue, 17 May 2016 14:42:47:  5000000 
INFO  @ Tue, 17 May 2016 14:42:49:  6000000 
INFO  @ Tue, 17 May 2016 14:42:51:  7000000 
INFO  @ Tue, 17 May 2016 14:42:53:  8000000 
INFO  @ Tue, 17 May 2016 14:42:55:  9000000 
INFO  @ Tue, 17 May 2016 14:42:57:  10000000 
INFO  @ Tue, 17 May 2016 14:42:59:  11000000 
INFO  @ Tue, 17 May 2016 14:43:01:  12000000 
INFO  @ Tue, 17 May 2016 14:43:03:  13000000 
INFO  @ Tue, 17 May 2016 14:43:05:  14000000 
INFO  @ Tue, 17 May 2016 14:43:07:  15000000 
INFO  @ Tue, 17 May 2016 14:43:09:  16000000 
INFO  @ Tue, 17 May 2016 14:43:11:  17000000 
INFO  @ Tue, 17 May 2016 14:43:13:  18000000 
INFO  @ Tue, 17 May 2016 14:43:15:  19000000 
INFO  @ Tue, 17 May 2016 14:43:17:  20000000 
INFO  @ Tue, 17 May 2016 14:43:19:  21000000 
INFO  @ Tue, 17 May 2016 14:43:21:  22000000 
INFO  @ Tue, 17 May 2016 14:43:23:  23000000 
INFO  @ Tue, 17 May 2016 14:43:25:  24000000 
INFO  @ Tue, 17 May 2016 14:43:27:  25000000 
INFO  @ Tue, 17 May 2016 14:43:29:  26000000 
INFO  @ Tue, 17 May 2016 14:43:30:  27000000 
INFO  @ Tue, 17 May 2016 14:43:32:  28000000 
INFO  @ Tue, 17 May 2016 14:43:34:  29000000 
INFO  @ Tue, 17 May 2016 14:43:36:  30000000 
INFO  @ Tue, 17 May 2016 14:43:38:  31000000 
INFO  @ Tue, 17 May 2016 14:43:40:  32000000 
INFO  @ Tue, 17 May 2016 14:43:42:  33000000 
INFO  @ Tue, 17 May 2016 14:43:44:  34000000 
INFO  @ Tue, 17 May 2016 14:43:46:  35000000 
INFO  @ Tue, 17 May 2016 14:43:48:  36000000 
INFO  @ Tue, 17 May 2016 14:43:50:  37000000 
INFO  @ Tue, 17 May 2016 14:43:52:  38000000 
INFO  @ Tue, 17 May 2016 14:43:54:  39000000 
INFO  @ Tue, 17 May 2016 14:43:56:  40000000 
INFO  @ Tue, 17 May 2016 14:44:00: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 14:44:00: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 14:44:00: #1  total tags in treatment: 40541222 
INFO  @ Tue, 17 May 2016 14:44:00: #1 finished! 
INFO  @ Tue, 17 May 2016 14:44:00: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:44:00: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:44:00: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:44:00: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:44:00: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:44:00: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 14:44:00: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 14:44:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:45:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 14:45:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 14:45:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 14:45:49: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 14:45:49: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:54:02: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 14:54:07: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 14:54:11: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 14:54:13: Done!

Num	30
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_35
Name	macs2_atac rep2
Thread	thread_21
PID	27905

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

Start	2016-05-17 14:36:12
End	2016-05-17 15:26:01
Elapsed	00:49:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:36:14: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:36:14: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:36:14: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:36:16:  1000000 
INFO  @ Tue, 17 May 2016 14:36:18:  2000000 
INFO  @ Tue, 17 May 2016 14:36:20:  3000000 
INFO  @ Tue, 17 May 2016 14:36:22:  4000000 
INFO  @ Tue, 17 May 2016 14:36:24:  5000000 
INFO  @ Tue, 17 May 2016 14:36:26:  6000000 
INFO  @ Tue, 17 May 2016 14:36:28:  7000000 
INFO  @ Tue, 17 May 2016 14:36:30:  8000000 
INFO  @ Tue, 17 May 2016 14:36:32:  9000000 
INFO  @ Tue, 17 May 2016 14:36:34:  10000000 
INFO  @ Tue, 17 May 2016 14:36:36:  11000000 
INFO  @ Tue, 17 May 2016 14:36:38:  12000000 
INFO  @ Tue, 17 May 2016 14:36:40:  13000000 
INFO  @ Tue, 17 May 2016 14:36:42:  14000000 
INFO  @ Tue, 17 May 2016 14:36:44:  15000000 
INFO  @ Tue, 17 May 2016 14:36:46:  16000000 
INFO  @ Tue, 17 May 2016 14:36:48:  17000000 
INFO  @ Tue, 17 May 2016 14:36:50:  18000000 
INFO  @ Tue, 17 May 2016 14:36:52:  19000000 
INFO  @ Tue, 17 May 2016 14:36:54:  20000000 
INFO  @ Tue, 17 May 2016 14:36:56:  21000000 
INFO  @ Tue, 17 May 2016 14:36:58:  22000000 
INFO  @ Tue, 17 May 2016 14:37:00:  23000000 
INFO  @ Tue, 17 May 2016 14:37:01:  24000000 
INFO  @ Tue, 17 May 2016 14:37:03:  25000000 
INFO  @ Tue, 17 May 2016 14:37:05:  26000000 
INFO  @ Tue, 17 May 2016 14:37:07:  27000000 
INFO  @ Tue, 17 May 2016 14:37:09:  28000000 
INFO  @ Tue, 17 May 2016 14:37:11:  29000000 
INFO  @ Tue, 17 May 2016 14:37:13:  30000000 
INFO  @ Tue, 17 May 2016 14:37:15:  31000000 
INFO  @ Tue, 17 May 2016 14:37:17:  32000000 
INFO  @ Tue, 17 May 2016 14:37:19:  33000000 
INFO  @ Tue, 17 May 2016 14:37:21:  34000000 
INFO  @ Tue, 17 May 2016 14:37:23:  35000000 
INFO  @ Tue, 17 May 2016 14:37:25:  36000000 
INFO  @ Tue, 17 May 2016 14:37:27:  37000000 
INFO  @ Tue, 17 May 2016 14:37:29:  38000000 
INFO  @ Tue, 17 May 2016 14:37:31:  39000000 
INFO  @ Tue, 17 May 2016 14:37:33:  40000000 
INFO  @ Tue, 17 May 2016 14:37:37: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 14:37:37: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 14:37:37: #1  total tags in treatment: 40541222 
INFO  @ Tue, 17 May 2016 14:37:37: #1 finished! 
INFO  @ Tue, 17 May 2016 14:37:37: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:37:37: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:37:37: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:37:37: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:37:37: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:37:37: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 14:37:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:39:16: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:42:00: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 14:42:03: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 14:42:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 14:42:07: Done! 
INFO  @ Tue, 17 May 2016 14:42:17: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 14:42:17: #1 read tag files... 
INFO  @ Tue, 17 May 2016 14:42:17: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 14:42:19:  1000000 
INFO  @ Tue, 17 May 2016 14:42:21:  2000000 
INFO  @ Tue, 17 May 2016 14:42:23:  3000000 
INFO  @ Tue, 17 May 2016 14:42:25:  4000000 
INFO  @ Tue, 17 May 2016 14:42:27:  5000000 
INFO  @ Tue, 17 May 2016 14:42:29:  6000000 
INFO  @ Tue, 17 May 2016 14:42:31:  7000000 
INFO  @ Tue, 17 May 2016 14:42:33:  8000000 
INFO  @ Tue, 17 May 2016 14:42:35:  9000000 
INFO  @ Tue, 17 May 2016 14:42:37:  10000000 
INFO  @ Tue, 17 May 2016 14:42:39:  11000000 
INFO  @ Tue, 17 May 2016 14:42:41:  12000000 
INFO  @ Tue, 17 May 2016 14:42:43:  13000000 
INFO  @ Tue, 17 May 2016 14:42:45:  14000000 
INFO  @ Tue, 17 May 2016 14:42:47:  15000000 
INFO  @ Tue, 17 May 2016 14:42:49:  16000000 
INFO  @ Tue, 17 May 2016 14:42:51:  17000000 
INFO  @ Tue, 17 May 2016 14:42:54:  18000000 
INFO  @ Tue, 17 May 2016 14:42:56:  19000000 
INFO  @ Tue, 17 May 2016 14:42:58:  20000000 
INFO  @ Tue, 17 May 2016 14:43:00:  21000000 
INFO  @ Tue, 17 May 2016 14:43:02:  22000000 
INFO  @ Tue, 17 May 2016 14:43:04:  23000000 
INFO  @ Tue, 17 May 2016 14:43:06:  24000000 
INFO  @ Tue, 17 May 2016 14:43:08:  25000000 
INFO  @ Tue, 17 May 2016 14:43:10:  26000000 
INFO  @ Tue, 17 May 2016 14:43:12:  27000000 
INFO  @ Tue, 17 May 2016 14:43:14:  28000000 
INFO  @ Tue, 17 May 2016 14:43:16:  29000000 
INFO  @ Tue, 17 May 2016 14:43:18:  30000000 
INFO  @ Tue, 17 May 2016 14:43:20:  31000000 
INFO  @ Tue, 17 May 2016 14:43:22:  32000000 
INFO  @ Tue, 17 May 2016 14:43:24:  33000000 
INFO  @ Tue, 17 May 2016 14:43:26:  34000000 
INFO  @ Tue, 17 May 2016 14:43:28:  35000000 
INFO  @ Tue, 17 May 2016 14:43:30:  36000000 
INFO  @ Tue, 17 May 2016 14:43:32:  37000000 
INFO  @ Tue, 17 May 2016 14:43:34:  38000000 
INFO  @ Tue, 17 May 2016 14:43:36:  39000000 
INFO  @ Tue, 17 May 2016 14:43:38:  40000000 
INFO  @ Tue, 17 May 2016 14:43:42: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 14:43:42: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 14:43:42: #1  total tags in treatment: 40541222 
INFO  @ Tue, 17 May 2016 14:43:42: #1 finished! 
INFO  @ Tue, 17 May 2016 14:43:42: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 14:43:42: #2 Skipped... 
INFO  @ Tue, 17 May 2016 14:43:42: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 14:43:42: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 14:43:42: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 14:43:42: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 14:43:42: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 14:43:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 14:45:19: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 14:45:19: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 14:45:19: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 14:45:19: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 14:45:19: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:51:40: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 14:51:43: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 14:51:45: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 14:51:46: Done! 
INFO  @ Tue, 17 May 2016 14:51:50: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 14:53:15: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 14:53:48: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 14:54:40: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 14:58:44: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 15:01:16: Finished 'FE'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 15:09:46: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 15:11:11: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 15:11:44: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 15:12:25: Values in your input bedGraph files will be multiplied by 40.541222 ... 
INFO  @ Tue, 17 May 2016 15:17:09: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 15:17:47: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 15:20:00: Finished 'ppois'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	44283

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

Start	2016-05-17 15:26:02
End	2016-05-17 15:28:38
Elapsed	00:02:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz  | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	44285

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

Start	2016-05-17 15:26:02
End	2016-05-17 15:27:26
Elapsed	00:01:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz  | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	44288

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

Start	2016-05-17 15:26:02
End	2016-05-17 15:27:27
Elapsed	00:01:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz  | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	44485

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

Start	2016-05-17 15:28:39
End	2016-05-17 15:57:27
Elapsed	00:28:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 15:28:42: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 15:28:42: #1 read tag files... 
INFO  @ Tue, 17 May 2016 15:28:42: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 15:28:44:  1000000 
INFO  @ Tue, 17 May 2016 15:28:46:  2000000 
INFO  @ Tue, 17 May 2016 15:28:48:  3000000 
INFO  @ Tue, 17 May 2016 15:28:50:  4000000 
INFO  @ Tue, 17 May 2016 15:28:52:  5000000 
INFO  @ Tue, 17 May 2016 15:28:55:  6000000 
INFO  @ Tue, 17 May 2016 15:28:57:  7000000 
INFO  @ Tue, 17 May 2016 15:28:59:  8000000 
INFO  @ Tue, 17 May 2016 15:29:01:  9000000 
INFO  @ Tue, 17 May 2016 15:29:03:  10000000 
INFO  @ Tue, 17 May 2016 15:29:05:  11000000 
INFO  @ Tue, 17 May 2016 15:29:07:  12000000 
INFO  @ Tue, 17 May 2016 15:29:09:  13000000 
INFO  @ Tue, 17 May 2016 15:29:11:  14000000 
INFO  @ Tue, 17 May 2016 15:29:14:  15000000 
INFO  @ Tue, 17 May 2016 15:29:16:  16000000 
INFO  @ Tue, 17 May 2016 15:29:18:  17000000 
INFO  @ Tue, 17 May 2016 15:29:20:  18000000 
INFO  @ Tue, 17 May 2016 15:29:22:  19000000 
INFO  @ Tue, 17 May 2016 15:29:24:  20000000 
INFO  @ Tue, 17 May 2016 15:29:26:  21000000 
INFO  @ Tue, 17 May 2016 15:29:28:  22000000 
INFO  @ Tue, 17 May 2016 15:29:30:  23000000 
INFO  @ Tue, 17 May 2016 15:29:33:  24000000 
INFO  @ Tue, 17 May 2016 15:29:35:  25000000 
INFO  @ Tue, 17 May 2016 15:29:37:  26000000 
INFO  @ Tue, 17 May 2016 15:29:39:  27000000 
INFO  @ Tue, 17 May 2016 15:29:41:  28000000 
INFO  @ Tue, 17 May 2016 15:29:43:  29000000 
INFO  @ Tue, 17 May 2016 15:29:45:  30000000 
INFO  @ Tue, 17 May 2016 15:29:47:  31000000 
INFO  @ Tue, 17 May 2016 15:29:49:  32000000 
INFO  @ Tue, 17 May 2016 15:29:51:  33000000 
INFO  @ Tue, 17 May 2016 15:29:53:  34000000 
INFO  @ Tue, 17 May 2016 15:29:55:  35000000 
INFO  @ Tue, 17 May 2016 15:29:58:  36000000 
INFO  @ Tue, 17 May 2016 15:29:59:  37000000 
INFO  @ Tue, 17 May 2016 15:30:02:  38000000 
INFO  @ Tue, 17 May 2016 15:30:04:  39000000 
INFO  @ Tue, 17 May 2016 15:30:06:  40000000 
INFO  @ Tue, 17 May 2016 15:30:08:  41000000 
INFO  @ Tue, 17 May 2016 15:30:10:  42000000 
INFO  @ Tue, 17 May 2016 15:30:12:  43000000 
INFO  @ Tue, 17 May 2016 15:30:14:  44000000 
INFO  @ Tue, 17 May 2016 15:30:16:  45000000 
INFO  @ Tue, 17 May 2016 15:30:18:  46000000 
INFO  @ Tue, 17 May 2016 15:30:20:  47000000 
INFO  @ Tue, 17 May 2016 15:30:22:  48000000 
INFO  @ Tue, 17 May 2016 15:30:24:  49000000 
INFO  @ Tue, 17 May 2016 15:30:26:  50000000 
INFO  @ Tue, 17 May 2016 15:30:29:  51000000 
INFO  @ Tue, 17 May 2016 15:30:31:  52000000 
INFO  @ Tue, 17 May 2016 15:30:33:  53000000 
INFO  @ Tue, 17 May 2016 15:30:35:  54000000 
INFO  @ Tue, 17 May 2016 15:30:37:  55000000 
INFO  @ Tue, 17 May 2016 15:30:39:  56000000 
INFO  @ Tue, 17 May 2016 15:30:41:  57000000 
INFO  @ Tue, 17 May 2016 15:30:43:  58000000 
INFO  @ Tue, 17 May 2016 15:30:45:  59000000 
INFO  @ Tue, 17 May 2016 15:30:47:  60000000 
INFO  @ Tue, 17 May 2016 15:30:49:  61000000 
INFO  @ Tue, 17 May 2016 15:30:51:  62000000 
INFO  @ Tue, 17 May 2016 15:30:53:  63000000 
INFO  @ Tue, 17 May 2016 15:30:55:  64000000 
INFO  @ Tue, 17 May 2016 15:30:58:  65000000 
INFO  @ Tue, 17 May 2016 15:31:00:  66000000 
INFO  @ Tue, 17 May 2016 15:31:02:  67000000 
INFO  @ Tue, 17 May 2016 15:31:04:  68000000 
INFO  @ Tue, 17 May 2016 15:31:06:  69000000 
INFO  @ Tue, 17 May 2016 15:31:08:  70000000 
INFO  @ Tue, 17 May 2016 15:31:10:  71000000 
INFO  @ Tue, 17 May 2016 15:31:12:  72000000 
INFO  @ Tue, 17 May 2016 15:31:14:  73000000 
INFO  @ Tue, 17 May 2016 15:31:16:  74000000 
INFO  @ Tue, 17 May 2016 15:31:18:  75000000 
INFO  @ Tue, 17 May 2016 15:31:20:  76000000 
INFO  @ Tue, 17 May 2016 15:31:22:  77000000 
INFO  @ Tue, 17 May 2016 15:31:24:  78000000 
INFO  @ Tue, 17 May 2016 15:31:26:  79000000 
INFO  @ Tue, 17 May 2016 15:31:28:  80000000 
INFO  @ Tue, 17 May 2016 15:31:30:  81000000 
INFO  @ Tue, 17 May 2016 15:31:32:  82000000 
INFO  @ Tue, 17 May 2016 15:31:34:  83000000 
INFO  @ Tue, 17 May 2016 15:31:36:  84000000 
INFO  @ Tue, 17 May 2016 15:31:38:  85000000 
INFO  @ Tue, 17 May 2016 15:31:40:  86000000 
INFO  @ Tue, 17 May 2016 15:31:41:  87000000 
INFO  @ Tue, 17 May 2016 15:31:43:  88000000 
INFO  @ Tue, 17 May 2016 15:31:45:  89000000 
INFO  @ Tue, 17 May 2016 15:31:47:  90000000 
INFO  @ Tue, 17 May 2016 15:31:49:  91000000 
INFO  @ Tue, 17 May 2016 15:31:57: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 15:31:57: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 15:31:57: #1  total tags in treatment: 91083484 
INFO  @ Tue, 17 May 2016 15:31:57: #1 finished! 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Skipped... 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 15:31:57: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 15:31:57: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 15:31:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 15:35:12: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 15:39:25: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 15:39:27: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 15:39:29: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 15:39:31: Done! 
INFO  @ Tue, 17 May 2016 15:39:40: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 15:39:40: #1 read tag files... 
INFO  @ Tue, 17 May 2016 15:39:40: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 15:39:42:  1000000 
INFO  @ Tue, 17 May 2016 15:39:44:  2000000 
INFO  @ Tue, 17 May 2016 15:39:46:  3000000 
INFO  @ Tue, 17 May 2016 15:39:48:  4000000 
INFO  @ Tue, 17 May 2016 15:39:50:  5000000 
INFO  @ Tue, 17 May 2016 15:39:52:  6000000 
INFO  @ Tue, 17 May 2016 15:39:54:  7000000 
INFO  @ Tue, 17 May 2016 15:39:56:  8000000 
INFO  @ Tue, 17 May 2016 15:39:58:  9000000 
INFO  @ Tue, 17 May 2016 15:39:59:  10000000 
INFO  @ Tue, 17 May 2016 15:40:01:  11000000 
INFO  @ Tue, 17 May 2016 15:40:03:  12000000 
INFO  @ Tue, 17 May 2016 15:40:05:  13000000 
INFO  @ Tue, 17 May 2016 15:40:07:  14000000 
INFO  @ Tue, 17 May 2016 15:40:09:  15000000 
INFO  @ Tue, 17 May 2016 15:40:11:  16000000 
INFO  @ Tue, 17 May 2016 15:40:13:  17000000 
INFO  @ Tue, 17 May 2016 15:40:15:  18000000 
INFO  @ Tue, 17 May 2016 15:40:17:  19000000 
INFO  @ Tue, 17 May 2016 15:40:19:  20000000 
INFO  @ Tue, 17 May 2016 15:40:21:  21000000 
INFO  @ Tue, 17 May 2016 15:40:23:  22000000 
INFO  @ Tue, 17 May 2016 15:40:25:  23000000 
INFO  @ Tue, 17 May 2016 15:40:27:  24000000 
INFO  @ Tue, 17 May 2016 15:40:28:  25000000 
INFO  @ Tue, 17 May 2016 15:40:30:  26000000 
INFO  @ Tue, 17 May 2016 15:40:32:  27000000 
INFO  @ Tue, 17 May 2016 15:40:34:  28000000 
INFO  @ Tue, 17 May 2016 15:40:36:  29000000 
INFO  @ Tue, 17 May 2016 15:40:38:  30000000 
INFO  @ Tue, 17 May 2016 15:40:40:  31000000 
INFO  @ Tue, 17 May 2016 15:40:42:  32000000 
INFO  @ Tue, 17 May 2016 15:40:44:  33000000 
INFO  @ Tue, 17 May 2016 15:40:46:  34000000 
INFO  @ Tue, 17 May 2016 15:40:48:  35000000 
INFO  @ Tue, 17 May 2016 15:40:50:  36000000 
INFO  @ Tue, 17 May 2016 15:40:52:  37000000 
INFO  @ Tue, 17 May 2016 15:40:54:  38000000 
INFO  @ Tue, 17 May 2016 15:40:56:  39000000 
INFO  @ Tue, 17 May 2016 15:40:58:  40000000 
INFO  @ Tue, 17 May 2016 15:41:00:  41000000 
INFO  @ Tue, 17 May 2016 15:41:02:  42000000 
INFO  @ Tue, 17 May 2016 15:41:04:  43000000 
INFO  @ Tue, 17 May 2016 15:41:06:  44000000 
INFO  @ Tue, 17 May 2016 15:41:08:  45000000 
INFO  @ Tue, 17 May 2016 15:41:10:  46000000 
INFO  @ Tue, 17 May 2016 15:41:12:  47000000 
INFO  @ Tue, 17 May 2016 15:41:14:  48000000 
INFO  @ Tue, 17 May 2016 15:41:16:  49000000 
INFO  @ Tue, 17 May 2016 15:41:18:  50000000 
INFO  @ Tue, 17 May 2016 15:41:19:  51000000 
INFO  @ Tue, 17 May 2016 15:41:21:  52000000 
INFO  @ Tue, 17 May 2016 15:41:23:  53000000 
INFO  @ Tue, 17 May 2016 15:41:25:  54000000 
INFO  @ Tue, 17 May 2016 15:41:27:  55000000 
INFO  @ Tue, 17 May 2016 15:41:29:  56000000 
INFO  @ Tue, 17 May 2016 15:41:31:  57000000 
INFO  @ Tue, 17 May 2016 15:41:33:  58000000 
INFO  @ Tue, 17 May 2016 15:41:35:  59000000 
INFO  @ Tue, 17 May 2016 15:41:37:  60000000 
INFO  @ Tue, 17 May 2016 15:41:39:  61000000 
INFO  @ Tue, 17 May 2016 15:41:41:  62000000 
INFO  @ Tue, 17 May 2016 15:41:43:  63000000 
INFO  @ Tue, 17 May 2016 15:41:45:  64000000 
INFO  @ Tue, 17 May 2016 15:41:47:  65000000 
INFO  @ Tue, 17 May 2016 15:41:48:  66000000 
INFO  @ Tue, 17 May 2016 15:41:50:  67000000 
INFO  @ Tue, 17 May 2016 15:41:52:  68000000 
INFO  @ Tue, 17 May 2016 15:41:54:  69000000 
INFO  @ Tue, 17 May 2016 15:41:56:  70000000 
INFO  @ Tue, 17 May 2016 15:41:58:  71000000 
INFO  @ Tue, 17 May 2016 15:42:00:  72000000 
INFO  @ Tue, 17 May 2016 15:42:02:  73000000 
INFO  @ Tue, 17 May 2016 15:42:04:  74000000 
INFO  @ Tue, 17 May 2016 15:42:06:  75000000 
INFO  @ Tue, 17 May 2016 15:42:08:  76000000 
INFO  @ Tue, 17 May 2016 15:42:10:  77000000 
INFO  @ Tue, 17 May 2016 15:42:12:  78000000 
INFO  @ Tue, 17 May 2016 15:42:14:  79000000 
INFO  @ Tue, 17 May 2016 15:42:16:  80000000 
INFO  @ Tue, 17 May 2016 15:42:17:  81000000 
INFO  @ Tue, 17 May 2016 15:42:19:  82000000 
INFO  @ Tue, 17 May 2016 15:42:21:  83000000 
INFO  @ Tue, 17 May 2016 15:42:23:  84000000 
INFO  @ Tue, 17 May 2016 15:42:25:  85000000 
INFO  @ Tue, 17 May 2016 15:42:27:  86000000 
INFO  @ Tue, 17 May 2016 15:42:29:  87000000 
INFO  @ Tue, 17 May 2016 15:42:31:  88000000 
INFO  @ Tue, 17 May 2016 15:42:33:  89000000 
INFO  @ Tue, 17 May 2016 15:42:35:  90000000 
INFO  @ Tue, 17 May 2016 15:42:37:  91000000 
INFO  @ Tue, 17 May 2016 15:42:44: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 15:42:44: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 15:42:44: #1  total tags in treatment: 91083484 
INFO  @ Tue, 17 May 2016 15:42:44: #1 finished! 
INFO  @ Tue, 17 May 2016 15:42:44: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 15:42:44: #2 Skipped... 
INFO  @ Tue, 17 May 2016 15:42:44: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 15:42:44: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 15:42:44: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 15:42:44: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 15:42:44: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 15:42:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 15:45:52: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 15:45:52: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 15:45:52: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 15:45:52: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 15:45:52: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 15:57:11: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 15:57:16: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 15:57:20: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 15:57:22: Done!

Num	35
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_40
Name	macs2_atac pooled
Thread	thread_Root
PID	44487

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

Start	2016-05-17 15:28:39
End	2016-05-17 16:58:02
Elapsed	01:29:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 15:28:42: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 15:28:42: #1 read tag files... 
INFO  @ Tue, 17 May 2016 15:28:42: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 15:28:44:  1000000 
INFO  @ Tue, 17 May 2016 15:28:46:  2000000 
INFO  @ Tue, 17 May 2016 15:28:48:  3000000 
INFO  @ Tue, 17 May 2016 15:28:50:  4000000 
INFO  @ Tue, 17 May 2016 15:28:52:  5000000 
INFO  @ Tue, 17 May 2016 15:28:55:  6000000 
INFO  @ Tue, 17 May 2016 15:28:57:  7000000 
INFO  @ Tue, 17 May 2016 15:28:59:  8000000 
INFO  @ Tue, 17 May 2016 15:29:01:  9000000 
INFO  @ Tue, 17 May 2016 15:29:03:  10000000 
INFO  @ Tue, 17 May 2016 15:29:05:  11000000 
INFO  @ Tue, 17 May 2016 15:29:07:  12000000 
INFO  @ Tue, 17 May 2016 15:29:09:  13000000 
INFO  @ Tue, 17 May 2016 15:29:11:  14000000 
INFO  @ Tue, 17 May 2016 15:29:13:  15000000 
INFO  @ Tue, 17 May 2016 15:29:15:  16000000 
INFO  @ Tue, 17 May 2016 15:29:17:  17000000 
INFO  @ Tue, 17 May 2016 15:29:20:  18000000 
INFO  @ Tue, 17 May 2016 15:29:22:  19000000 
INFO  @ Tue, 17 May 2016 15:29:24:  20000000 
INFO  @ Tue, 17 May 2016 15:29:26:  21000000 
INFO  @ Tue, 17 May 2016 15:29:28:  22000000 
INFO  @ Tue, 17 May 2016 15:29:30:  23000000 
INFO  @ Tue, 17 May 2016 15:29:32:  24000000 
INFO  @ Tue, 17 May 2016 15:29:34:  25000000 
INFO  @ Tue, 17 May 2016 15:29:36:  26000000 
INFO  @ Tue, 17 May 2016 15:29:38:  27000000 
INFO  @ Tue, 17 May 2016 15:29:40:  28000000 
INFO  @ Tue, 17 May 2016 15:29:42:  29000000 
INFO  @ Tue, 17 May 2016 15:29:45:  30000000 
INFO  @ Tue, 17 May 2016 15:29:47:  31000000 
INFO  @ Tue, 17 May 2016 15:29:49:  32000000 
INFO  @ Tue, 17 May 2016 15:29:51:  33000000 
INFO  @ Tue, 17 May 2016 15:29:53:  34000000 
INFO  @ Tue, 17 May 2016 15:29:55:  35000000 
INFO  @ Tue, 17 May 2016 15:29:57:  36000000 
INFO  @ Tue, 17 May 2016 15:29:59:  37000000 
INFO  @ Tue, 17 May 2016 15:30:01:  38000000 
INFO  @ Tue, 17 May 2016 15:30:03:  39000000 
INFO  @ Tue, 17 May 2016 15:30:05:  40000000 
INFO  @ Tue, 17 May 2016 15:30:07:  41000000 
INFO  @ Tue, 17 May 2016 15:30:09:  42000000 
INFO  @ Tue, 17 May 2016 15:30:11:  43000000 
INFO  @ Tue, 17 May 2016 15:30:13:  44000000 
INFO  @ Tue, 17 May 2016 15:30:15:  45000000 
INFO  @ Tue, 17 May 2016 15:30:18:  46000000 
INFO  @ Tue, 17 May 2016 15:30:20:  47000000 
INFO  @ Tue, 17 May 2016 15:30:22:  48000000 
INFO  @ Tue, 17 May 2016 15:30:24:  49000000 
INFO  @ Tue, 17 May 2016 15:30:26:  50000000 
INFO  @ Tue, 17 May 2016 15:30:28:  51000000 
INFO  @ Tue, 17 May 2016 15:30:30:  52000000 
INFO  @ Tue, 17 May 2016 15:30:32:  53000000 
INFO  @ Tue, 17 May 2016 15:30:34:  54000000 
INFO  @ Tue, 17 May 2016 15:30:36:  55000000 
INFO  @ Tue, 17 May 2016 15:30:38:  56000000 
INFO  @ Tue, 17 May 2016 15:30:40:  57000000 
INFO  @ Tue, 17 May 2016 15:30:43:  58000000 
INFO  @ Tue, 17 May 2016 15:30:45:  59000000 
INFO  @ Tue, 17 May 2016 15:30:47:  60000000 
INFO  @ Tue, 17 May 2016 15:30:49:  61000000 
INFO  @ Tue, 17 May 2016 15:30:51:  62000000 
INFO  @ Tue, 17 May 2016 15:30:53:  63000000 
INFO  @ Tue, 17 May 2016 15:30:55:  64000000 
INFO  @ Tue, 17 May 2016 15:30:57:  65000000 
INFO  @ Tue, 17 May 2016 15:30:59:  66000000 
INFO  @ Tue, 17 May 2016 15:31:01:  67000000 
INFO  @ Tue, 17 May 2016 15:31:03:  68000000 
INFO  @ Tue, 17 May 2016 15:31:05:  69000000 
INFO  @ Tue, 17 May 2016 15:31:07:  70000000 
INFO  @ Tue, 17 May 2016 15:31:10:  71000000 
INFO  @ Tue, 17 May 2016 15:31:12:  72000000 
INFO  @ Tue, 17 May 2016 15:31:14:  73000000 
INFO  @ Tue, 17 May 2016 15:31:16:  74000000 
INFO  @ Tue, 17 May 2016 15:31:18:  75000000 
INFO  @ Tue, 17 May 2016 15:31:20:  76000000 
INFO  @ Tue, 17 May 2016 15:31:22:  77000000 
INFO  @ Tue, 17 May 2016 15:31:24:  78000000 
INFO  @ Tue, 17 May 2016 15:31:26:  79000000 
INFO  @ Tue, 17 May 2016 15:31:28:  80000000 
INFO  @ Tue, 17 May 2016 15:31:30:  81000000 
INFO  @ Tue, 17 May 2016 15:31:32:  82000000 
INFO  @ Tue, 17 May 2016 15:31:33:  83000000 
INFO  @ Tue, 17 May 2016 15:31:35:  84000000 
INFO  @ Tue, 17 May 2016 15:31:37:  85000000 
INFO  @ Tue, 17 May 2016 15:31:39:  86000000 
INFO  @ Tue, 17 May 2016 15:31:41:  87000000 
INFO  @ Tue, 17 May 2016 15:31:43:  88000000 
INFO  @ Tue, 17 May 2016 15:31:45:  89000000 
INFO  @ Tue, 17 May 2016 15:31:47:  90000000 
INFO  @ Tue, 17 May 2016 15:31:49:  91000000 
INFO  @ Tue, 17 May 2016 15:31:57: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 15:31:57: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 15:31:57: #1  total tags in treatment: 91083484 
INFO  @ Tue, 17 May 2016 15:31:57: #1 finished! 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Skipped... 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 15:31:57: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 15:31:57: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 15:31:57: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 15:31:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 15:35:12: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 15:39:07: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 15:39:09: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 15:39:11: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 15:39:13: Done! 
INFO  @ Tue, 17 May 2016 15:39:22: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 15:39:22: #1 read tag files... 
INFO  @ Tue, 17 May 2016 15:39:22: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 15:39:24:  1000000 
INFO  @ Tue, 17 May 2016 15:39:26:  2000000 
INFO  @ Tue, 17 May 2016 15:39:28:  3000000 
INFO  @ Tue, 17 May 2016 15:39:30:  4000000 
INFO  @ Tue, 17 May 2016 15:39:32:  5000000 
INFO  @ Tue, 17 May 2016 15:39:34:  6000000 
INFO  @ Tue, 17 May 2016 15:39:36:  7000000 
INFO  @ Tue, 17 May 2016 15:39:38:  8000000 
INFO  @ Tue, 17 May 2016 15:39:40:  9000000 
INFO  @ Tue, 17 May 2016 15:39:42:  10000000 
INFO  @ Tue, 17 May 2016 15:39:43:  11000000 
INFO  @ Tue, 17 May 2016 15:39:45:  12000000 
INFO  @ Tue, 17 May 2016 15:39:47:  13000000 
INFO  @ Tue, 17 May 2016 15:39:49:  14000000 
INFO  @ Tue, 17 May 2016 15:39:51:  15000000 
INFO  @ Tue, 17 May 2016 15:39:53:  16000000 
INFO  @ Tue, 17 May 2016 15:39:55:  17000000 
INFO  @ Tue, 17 May 2016 15:39:57:  18000000 
INFO  @ Tue, 17 May 2016 15:39:59:  19000000 
INFO  @ Tue, 17 May 2016 15:40:01:  20000000 
INFO  @ Tue, 17 May 2016 15:40:03:  21000000 
INFO  @ Tue, 17 May 2016 15:40:05:  22000000 
INFO  @ Tue, 17 May 2016 15:40:07:  23000000 
INFO  @ Tue, 17 May 2016 15:40:09:  24000000 
INFO  @ Tue, 17 May 2016 15:40:10:  25000000 
INFO  @ Tue, 17 May 2016 15:40:12:  26000000 
INFO  @ Tue, 17 May 2016 15:40:14:  27000000 
INFO  @ Tue, 17 May 2016 15:40:16:  28000000 
INFO  @ Tue, 17 May 2016 15:40:18:  29000000 
INFO  @ Tue, 17 May 2016 15:40:20:  30000000 
INFO  @ Tue, 17 May 2016 15:40:22:  31000000 
INFO  @ Tue, 17 May 2016 15:40:24:  32000000 
INFO  @ Tue, 17 May 2016 15:40:26:  33000000 
INFO  @ Tue, 17 May 2016 15:40:28:  34000000 
INFO  @ Tue, 17 May 2016 15:40:30:  35000000 
INFO  @ Tue, 17 May 2016 15:40:32:  36000000 
INFO  @ Tue, 17 May 2016 15:40:34:  37000000 
INFO  @ Tue, 17 May 2016 15:40:36:  38000000 
INFO  @ Tue, 17 May 2016 15:40:38:  39000000 
INFO  @ Tue, 17 May 2016 15:40:40:  40000000 
INFO  @ Tue, 17 May 2016 15:40:42:  41000000 
INFO  @ Tue, 17 May 2016 15:40:44:  42000000 
INFO  @ Tue, 17 May 2016 15:40:45:  43000000 
INFO  @ Tue, 17 May 2016 15:40:47:  44000000 
INFO  @ Tue, 17 May 2016 15:40:49:  45000000 
INFO  @ Tue, 17 May 2016 15:40:51:  46000000 
INFO  @ Tue, 17 May 2016 15:40:53:  47000000 
INFO  @ Tue, 17 May 2016 15:40:55:  48000000 
INFO  @ Tue, 17 May 2016 15:40:57:  49000000 
INFO  @ Tue, 17 May 2016 15:40:59:  50000000 
INFO  @ Tue, 17 May 2016 15:41:01:  51000000 
INFO  @ Tue, 17 May 2016 15:41:03:  52000000 
INFO  @ Tue, 17 May 2016 15:41:04:  53000000 
INFO  @ Tue, 17 May 2016 15:41:06:  54000000 
INFO  @ Tue, 17 May 2016 15:41:08:  55000000 
INFO  @ Tue, 17 May 2016 15:41:10:  56000000 
INFO  @ Tue, 17 May 2016 15:41:12:  57000000 
INFO  @ Tue, 17 May 2016 15:41:14:  58000000 
INFO  @ Tue, 17 May 2016 15:41:16:  59000000 
INFO  @ Tue, 17 May 2016 15:41:18:  60000000 
INFO  @ Tue, 17 May 2016 15:41:20:  61000000 
INFO  @ Tue, 17 May 2016 15:41:21:  62000000 
INFO  @ Tue, 17 May 2016 15:41:23:  63000000 
INFO  @ Tue, 17 May 2016 15:41:25:  64000000 
INFO  @ Tue, 17 May 2016 15:41:27:  65000000 
INFO  @ Tue, 17 May 2016 15:41:29:  66000000 
INFO  @ Tue, 17 May 2016 15:41:31:  67000000 
INFO  @ Tue, 17 May 2016 15:41:33:  68000000 
INFO  @ Tue, 17 May 2016 15:41:35:  69000000 
INFO  @ Tue, 17 May 2016 15:41:37:  70000000 
INFO  @ Tue, 17 May 2016 15:41:38:  71000000 
INFO  @ Tue, 17 May 2016 15:41:40:  72000000 
INFO  @ Tue, 17 May 2016 15:41:42:  73000000 
INFO  @ Tue, 17 May 2016 15:41:44:  74000000 
INFO  @ Tue, 17 May 2016 15:41:46:  75000000 
INFO  @ Tue, 17 May 2016 15:41:48:  76000000 
INFO  @ Tue, 17 May 2016 15:41:50:  77000000 
INFO  @ Tue, 17 May 2016 15:41:52:  78000000 
INFO  @ Tue, 17 May 2016 15:41:53:  79000000 
INFO  @ Tue, 17 May 2016 15:41:55:  80000000 
INFO  @ Tue, 17 May 2016 15:41:57:  81000000 
INFO  @ Tue, 17 May 2016 15:41:59:  82000000 
INFO  @ Tue, 17 May 2016 15:42:01:  83000000 
INFO  @ Tue, 17 May 2016 15:42:03:  84000000 
INFO  @ Tue, 17 May 2016 15:42:05:  85000000 
INFO  @ Tue, 17 May 2016 15:42:07:  86000000 
INFO  @ Tue, 17 May 2016 15:42:09:  87000000 
INFO  @ Tue, 17 May 2016 15:42:10:  88000000 
INFO  @ Tue, 17 May 2016 15:42:12:  89000000 
INFO  @ Tue, 17 May 2016 15:42:14:  90000000 
INFO  @ Tue, 17 May 2016 15:42:16:  91000000 
INFO  @ Tue, 17 May 2016 15:42:24: #1 tag size is determined as 65 bps 
INFO  @ Tue, 17 May 2016 15:42:24: #1 tag size = 65 
INFO  @ Tue, 17 May 2016 15:42:24: #1  total tags in treatment: 91083484 
INFO  @ Tue, 17 May 2016 15:42:24: #1 finished! 
INFO  @ Tue, 17 May 2016 15:42:24: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 15:42:24: #2 Skipped... 
INFO  @ Tue, 17 May 2016 15:42:24: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 15:42:24: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 15:42:24: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 15:42:24: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 15:42:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 15:42:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 15:45:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 15:45:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 15:45:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 15:45:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 15:45:33: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 15:55:52: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 15:55:55: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 15:55:58: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_summits.bed 
INFO  @ Tue, 17 May 2016 15:55:59: Done! 
INFO  @ Tue, 17 May 2016 15:56:04: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 15:58:47: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 15:59:42: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 16:00:41: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 16:09:17: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 16:14:09: Finished 'FE'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 16:27:46: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 16:30:29: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 16:31:24: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 16:32:22: Values in your input bedGraph files will be multiplied by 91.083484 ... 
INFO  @ Tue, 17 May 2016 16:39:50: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 16:41:11: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 16:45:43: Finished 'ppois'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	37037

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

Start	2016-05-17 16:58:03
End	2016-05-17 17:16:32
Elapsed	00:18:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 16:58:06: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 16:58:06: #1 read tag files... 
INFO  @ Tue, 17 May 2016 16:58:06: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 16:58:08:  1000000 
INFO  @ Tue, 17 May 2016 16:58:10:  2000000 
INFO  @ Tue, 17 May 2016 16:58:12:  3000000 
INFO  @ Tue, 17 May 2016 16:58:14:  4000000 
INFO  @ Tue, 17 May 2016 16:58:16:  5000000 
INFO  @ Tue, 17 May 2016 16:58:18:  6000000 
INFO  @ Tue, 17 May 2016 16:58:20:  7000000 
INFO  @ Tue, 17 May 2016 16:58:22:  8000000 
INFO  @ Tue, 17 May 2016 16:58:23:  9000000 
INFO  @ Tue, 17 May 2016 16:58:25:  10000000 
INFO  @ Tue, 17 May 2016 16:58:27:  11000000 
INFO  @ Tue, 17 May 2016 16:58:29:  12000000 
INFO  @ Tue, 17 May 2016 16:58:31:  13000000 
INFO  @ Tue, 17 May 2016 16:58:33:  14000000 
INFO  @ Tue, 17 May 2016 16:58:35:  15000000 
INFO  @ Tue, 17 May 2016 16:58:37:  16000000 
INFO  @ Tue, 17 May 2016 16:58:39:  17000000 
INFO  @ Tue, 17 May 2016 16:58:41:  18000000 
INFO  @ Tue, 17 May 2016 16:58:42:  19000000 
INFO  @ Tue, 17 May 2016 16:58:44:  20000000 
INFO  @ Tue, 17 May 2016 16:58:46:  21000000 
INFO  @ Tue, 17 May 2016 16:58:48:  22000000 
INFO  @ Tue, 17 May 2016 16:58:50:  23000000 
INFO  @ Tue, 17 May 2016 16:58:52:  24000000 
INFO  @ Tue, 17 May 2016 16:58:54:  25000000 
INFO  @ Tue, 17 May 2016 16:58:56:  26000000 
INFO  @ Tue, 17 May 2016 16:58:58:  27000000 
INFO  @ Tue, 17 May 2016 16:59:00:  28000000 
INFO  @ Tue, 17 May 2016 16:59:02:  29000000 
INFO  @ Tue, 17 May 2016 16:59:04:  30000000 
INFO  @ Tue, 17 May 2016 16:59:06:  31000000 
INFO  @ Tue, 17 May 2016 16:59:08:  32000000 
INFO  @ Tue, 17 May 2016 16:59:09:  33000000 
INFO  @ Tue, 17 May 2016 16:59:11:  34000000 
INFO  @ Tue, 17 May 2016 16:59:13:  35000000 
INFO  @ Tue, 17 May 2016 16:59:15:  36000000 
INFO  @ Tue, 17 May 2016 16:59:17:  37000000 
INFO  @ Tue, 17 May 2016 16:59:19:  38000000 
INFO  @ Tue, 17 May 2016 16:59:21:  39000000 
INFO  @ Tue, 17 May 2016 16:59:23:  40000000 
INFO  @ Tue, 17 May 2016 16:59:25:  41000000 
INFO  @ Tue, 17 May 2016 16:59:27:  42000000 
INFO  @ Tue, 17 May 2016 16:59:28:  43000000 
INFO  @ Tue, 17 May 2016 16:59:30:  44000000 
INFO  @ Tue, 17 May 2016 16:59:32:  45000000 
INFO  @ Tue, 17 May 2016 16:59:34:  46000000 
INFO  @ Tue, 17 May 2016 16:59:36:  47000000 
INFO  @ Tue, 17 May 2016 16:59:38:  48000000 
INFO  @ Tue, 17 May 2016 16:59:40:  49000000 
INFO  @ Tue, 17 May 2016 16:59:45: #1 tag size is determined as 56 bps 
INFO  @ Tue, 17 May 2016 16:59:45: #1 tag size = 56 
INFO  @ Tue, 17 May 2016 16:59:45: #1  total tags in treatment: 49508156 
INFO  @ Tue, 17 May 2016 16:59:45: #1 finished! 
INFO  @ Tue, 17 May 2016 16:59:45: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 16:59:45: #2 Skipped... 
INFO  @ Tue, 17 May 2016 16:59:45: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 16:59:45: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 16:59:45: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 16:59:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 16:59:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 17:02:00: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 17:04:34: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 17:04:37: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 17:04:39: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 17:04:41: Done! 
INFO  @ Tue, 17 May 2016 17:04:50: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 17:04:50: #1 read tag files... 
INFO  @ Tue, 17 May 2016 17:04:50: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 17:04:52:  1000000 
INFO  @ Tue, 17 May 2016 17:04:54:  2000000 
INFO  @ Tue, 17 May 2016 17:04:56:  3000000 
INFO  @ Tue, 17 May 2016 17:04:58:  4000000 
INFO  @ Tue, 17 May 2016 17:04:59:  5000000 
INFO  @ Tue, 17 May 2016 17:05:01:  6000000 
INFO  @ Tue, 17 May 2016 17:05:03:  7000000 
INFO  @ Tue, 17 May 2016 17:05:05:  8000000 
INFO  @ Tue, 17 May 2016 17:05:07:  9000000 
INFO  @ Tue, 17 May 2016 17:05:09:  10000000 
INFO  @ Tue, 17 May 2016 17:05:11:  11000000 
INFO  @ Tue, 17 May 2016 17:05:13:  12000000 
INFO  @ Tue, 17 May 2016 17:05:15:  13000000 
INFO  @ Tue, 17 May 2016 17:05:17:  14000000 
INFO  @ Tue, 17 May 2016 17:05:19:  15000000 
INFO  @ Tue, 17 May 2016 17:05:21:  16000000 
INFO  @ Tue, 17 May 2016 17:05:23:  17000000 
INFO  @ Tue, 17 May 2016 17:05:25:  18000000 
INFO  @ Tue, 17 May 2016 17:05:27:  19000000 
INFO  @ Tue, 17 May 2016 17:05:29:  20000000 
INFO  @ Tue, 17 May 2016 17:05:31:  21000000 
INFO  @ Tue, 17 May 2016 17:05:32:  22000000 
INFO  @ Tue, 17 May 2016 17:05:34:  23000000 
INFO  @ Tue, 17 May 2016 17:05:36:  24000000 
INFO  @ Tue, 17 May 2016 17:05:38:  25000000 
INFO  @ Tue, 17 May 2016 17:05:40:  26000000 
INFO  @ Tue, 17 May 2016 17:05:42:  27000000 
INFO  @ Tue, 17 May 2016 17:05:44:  28000000 
INFO  @ Tue, 17 May 2016 17:05:46:  29000000 
INFO  @ Tue, 17 May 2016 17:05:48:  30000000 
INFO  @ Tue, 17 May 2016 17:05:50:  31000000 
INFO  @ Tue, 17 May 2016 17:05:52:  32000000 
INFO  @ Tue, 17 May 2016 17:05:54:  33000000 
INFO  @ Tue, 17 May 2016 17:05:56:  34000000 
INFO  @ Tue, 17 May 2016 17:05:58:  35000000 
INFO  @ Tue, 17 May 2016 17:06:00:  36000000 
INFO  @ Tue, 17 May 2016 17:06:02:  37000000 
INFO  @ Tue, 17 May 2016 17:06:03:  38000000 
INFO  @ Tue, 17 May 2016 17:06:05:  39000000 
INFO  @ Tue, 17 May 2016 17:06:07:  40000000 
INFO  @ Tue, 17 May 2016 17:06:09:  41000000 
INFO  @ Tue, 17 May 2016 17:06:11:  42000000 
INFO  @ Tue, 17 May 2016 17:06:13:  43000000 
INFO  @ Tue, 17 May 2016 17:06:15:  44000000 
INFO  @ Tue, 17 May 2016 17:06:17:  45000000 
INFO  @ Tue, 17 May 2016 17:06:19:  46000000 
INFO  @ Tue, 17 May 2016 17:06:21:  47000000 
INFO  @ Tue, 17 May 2016 17:06:22:  48000000 
INFO  @ Tue, 17 May 2016 17:06:24:  49000000 
INFO  @ Tue, 17 May 2016 17:06:29: #1 tag size is determined as 56 bps 
INFO  @ Tue, 17 May 2016 17:06:29: #1 tag size = 56 
INFO  @ Tue, 17 May 2016 17:06:29: #1  total tags in treatment: 49508156 
INFO  @ Tue, 17 May 2016 17:06:29: #1 finished! 
INFO  @ Tue, 17 May 2016 17:06:29: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 17:06:29: #2 Skipped... 
INFO  @ Tue, 17 May 2016 17:06:29: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 17:06:29: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 17:06:29: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 17:06:29: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 17:06:29: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 17:06:29: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 17:08:41: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 17:08:41: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 17:08:41: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 17:08:41: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 17:08:41: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 17:16:17: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 17:16:22: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 17:16:26: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 17:16:27: 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	37039

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

Start	2016-05-17 16:58:03
End	2016-05-17 17:16:27
Elapsed	00:18:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 16:58:06: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 16:58:06: #1 read tag files... 
INFO  @ Tue, 17 May 2016 16:58:06: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 16:58:08:  1000000 
INFO  @ Tue, 17 May 2016 16:58:10:  2000000 
INFO  @ Tue, 17 May 2016 16:58:12:  3000000 
INFO  @ Tue, 17 May 2016 16:58:14:  4000000 
INFO  @ Tue, 17 May 2016 16:58:16:  5000000 
INFO  @ Tue, 17 May 2016 16:58:18:  6000000 
INFO  @ Tue, 17 May 2016 16:58:19:  7000000 
INFO  @ Tue, 17 May 2016 16:58:21:  8000000 
INFO  @ Tue, 17 May 2016 16:58:23:  9000000 
INFO  @ Tue, 17 May 2016 16:58:25:  10000000 
INFO  @ Tue, 17 May 2016 16:58:27:  11000000 
INFO  @ Tue, 17 May 2016 16:58:29:  12000000 
INFO  @ Tue, 17 May 2016 16:58:31:  13000000 
INFO  @ Tue, 17 May 2016 16:58:33:  14000000 
INFO  @ Tue, 17 May 2016 16:58:35:  15000000 
INFO  @ Tue, 17 May 2016 16:58:37:  16000000 
INFO  @ Tue, 17 May 2016 16:58:39:  17000000 
INFO  @ Tue, 17 May 2016 16:58:40:  18000000 
INFO  @ Tue, 17 May 2016 16:58:42:  19000000 
INFO  @ Tue, 17 May 2016 16:58:44:  20000000 
INFO  @ Tue, 17 May 2016 16:58:46:  21000000 
INFO  @ Tue, 17 May 2016 16:58:48:  22000000 
INFO  @ Tue, 17 May 2016 16:58:50:  23000000 
INFO  @ Tue, 17 May 2016 16:58:52:  24000000 
INFO  @ Tue, 17 May 2016 16:58:54:  25000000 
INFO  @ Tue, 17 May 2016 16:58:56:  26000000 
INFO  @ Tue, 17 May 2016 16:58:58:  27000000 
INFO  @ Tue, 17 May 2016 16:58:59:  28000000 
INFO  @ Tue, 17 May 2016 16:59:01:  29000000 
INFO  @ Tue, 17 May 2016 16:59:03:  30000000 
INFO  @ Tue, 17 May 2016 16:59:05:  31000000 
INFO  @ Tue, 17 May 2016 16:59:07:  32000000 
INFO  @ Tue, 17 May 2016 16:59:09:  33000000 
INFO  @ Tue, 17 May 2016 16:59:11:  34000000 
INFO  @ Tue, 17 May 2016 16:59:13:  35000000 
INFO  @ Tue, 17 May 2016 16:59:15:  36000000 
INFO  @ Tue, 17 May 2016 16:59:16:  37000000 
INFO  @ Tue, 17 May 2016 16:59:18:  38000000 
INFO  @ Tue, 17 May 2016 16:59:20:  39000000 
INFO  @ Tue, 17 May 2016 16:59:22:  40000000 
INFO  @ Tue, 17 May 2016 16:59:24:  41000000 
INFO  @ Tue, 17 May 2016 16:59:26:  42000000 
INFO  @ Tue, 17 May 2016 16:59:28:  43000000 
INFO  @ Tue, 17 May 2016 16:59:30:  44000000 
INFO  @ Tue, 17 May 2016 16:59:32:  45000000 
INFO  @ Tue, 17 May 2016 16:59:33:  46000000 
INFO  @ Tue, 17 May 2016 16:59:35:  47000000 
INFO  @ Tue, 17 May 2016 16:59:37:  48000000 
INFO  @ Tue, 17 May 2016 16:59:39:  49000000 
INFO  @ Tue, 17 May 2016 16:59:44: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 16:59:44: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 16:59:44: #1  total tags in treatment: 49508156 
INFO  @ Tue, 17 May 2016 16:59:44: #1 finished! 
INFO  @ Tue, 17 May 2016 16:59:44: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 16:59:44: #2 Skipped... 
INFO  @ Tue, 17 May 2016 16:59:44: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 16:59:44: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 16:59:44: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 16:59:44: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 16:59:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 17:01:59: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 17:04:30: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 17:04:33: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 17:04:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 17:04:37: Done! 
INFO  @ Tue, 17 May 2016 17:04:46: 
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 17:04:46: #1 read tag files... 
INFO  @ Tue, 17 May 2016 17:04:46: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 17:04:48:  1000000 
INFO  @ Tue, 17 May 2016 17:04:50:  2000000 
INFO  @ Tue, 17 May 2016 17:04:52:  3000000 
INFO  @ Tue, 17 May 2016 17:04:54:  4000000 
INFO  @ Tue, 17 May 2016 17:04:56:  5000000 
INFO  @ Tue, 17 May 2016 17:04:57:  6000000 
INFO  @ Tue, 17 May 2016 17:04:59:  7000000 
INFO  @ Tue, 17 May 2016 17:05:01:  8000000 
INFO  @ Tue, 17 May 2016 17:05:03:  9000000 
INFO  @ Tue, 17 May 2016 17:05:05:  10000000 
INFO  @ Tue, 17 May 2016 17:05:07:  11000000 
INFO  @ Tue, 17 May 2016 17:05:09:  12000000 
INFO  @ Tue, 17 May 2016 17:05:11:  13000000 
INFO  @ Tue, 17 May 2016 17:05:13:  14000000 
INFO  @ Tue, 17 May 2016 17:05:15:  15000000 
INFO  @ Tue, 17 May 2016 17:05:17:  16000000 
INFO  @ Tue, 17 May 2016 17:05:19:  17000000 
INFO  @ Tue, 17 May 2016 17:05:21:  18000000 
INFO  @ Tue, 17 May 2016 17:05:23:  19000000 
INFO  @ Tue, 17 May 2016 17:05:24:  20000000 
INFO  @ Tue, 17 May 2016 17:05:26:  21000000 
INFO  @ Tue, 17 May 2016 17:05:28:  22000000 
INFO  @ Tue, 17 May 2016 17:05:30:  23000000 
INFO  @ Tue, 17 May 2016 17:05:32:  24000000 
INFO  @ Tue, 17 May 2016 17:05:34:  25000000 
INFO  @ Tue, 17 May 2016 17:05:36:  26000000 
INFO  @ Tue, 17 May 2016 17:05:38:  27000000 
INFO  @ Tue, 17 May 2016 17:05:40:  28000000 
INFO  @ Tue, 17 May 2016 17:05:42:  29000000 
INFO  @ Tue, 17 May 2016 17:05:43:  30000000 
INFO  @ Tue, 17 May 2016 17:05:45:  31000000 
INFO  @ Tue, 17 May 2016 17:05:47:  32000000 
INFO  @ Tue, 17 May 2016 17:05:49:  33000000 
INFO  @ Tue, 17 May 2016 17:05:51:  34000000 
INFO  @ Tue, 17 May 2016 17:05:53:  35000000 
INFO  @ Tue, 17 May 2016 17:05:55:  36000000 
INFO  @ Tue, 17 May 2016 17:05:56:  37000000 
INFO  @ Tue, 17 May 2016 17:05:58:  38000000 
INFO  @ Tue, 17 May 2016 17:06:00:  39000000 
INFO  @ Tue, 17 May 2016 17:06:02:  40000000 
INFO  @ Tue, 17 May 2016 17:06:04:  41000000 
INFO  @ Tue, 17 May 2016 17:06:06:  42000000 
INFO  @ Tue, 17 May 2016 17:06:08:  43000000 
INFO  @ Tue, 17 May 2016 17:06:09:  44000000 
INFO  @ Tue, 17 May 2016 17:06:11:  45000000 
INFO  @ Tue, 17 May 2016 17:06:13:  46000000 
INFO  @ Tue, 17 May 2016 17:06:15:  47000000 
INFO  @ Tue, 17 May 2016 17:06:17:  48000000 
INFO  @ Tue, 17 May 2016 17:06:19:  49000000 
INFO  @ Tue, 17 May 2016 17:06:23: #1 tag size is determined as 70 bps 
INFO  @ Tue, 17 May 2016 17:06:23: #1 tag size = 70 
INFO  @ Tue, 17 May 2016 17:06:23: #1  total tags in treatment: 49508156 
INFO  @ Tue, 17 May 2016 17:06:23: #1 finished! 
INFO  @ Tue, 17 May 2016 17:06:23: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 17:06:23: #2 Skipped... 
INFO  @ Tue, 17 May 2016 17:06:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 17:06:23: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 17:06:23: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 17:06:23: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 17:06:23: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 17:06:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 17:08:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 17:08:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 17:08:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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  @ Tue, 17 May 2016 17:08:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 17:08:33: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 17:16:13: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 17:16:18: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 17:16:21: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_pseudo_reps/ppr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 17:16:23: Done!

Num	38
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_43
Name	filt_top_peaks rep1
Thread	thread_Root
PID	43655

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:40
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43660

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43668

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:40
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43679

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:41
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43692

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:40
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43710

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:40
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43725

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:40
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43739

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43750

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43764

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43792

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43805

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43823

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:40
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43837

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43862

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43880

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

Start	2016-05-17 17:16:32
End	2016-05-17 17:16:39
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43901

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

Start	2016-05-17 17:16:33
End	2016-05-17 17:16:39
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	43916

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

Start	2016-05-17 17:16:33
End	2016-05-17 17:16:39
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	44752

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

Start	2016-05-17 17:16:41
End	2016-05-17 17:16:43
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	3367.55273	135
ERROR: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	5609.20996	143
ERROR: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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:
chr1	565551	565839	Peak_2	46131	.	39.21295	4613.11523	4605.73145	144
ERROR: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	14668	16606	Peak_2	49068	.	2.72916	4906.88037	4899.11621	1104

Num	57
ID	task.callpeak_etc.naive_overlap_thresh_gpeak.line_125.id_62
Name	naive_overlap_thresh gpeak
Thread	thread_Root
PID	44757

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

Start	2016-05-17 17:16:41
End	2016-05-17 17:16:43
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/pooled_rep/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	197066766	197068289	Peak_354592	4	.	197066766	197068289	0	2	1,811	0,712	1.28939	1.34578	0.40640
ERROR: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_52157	188	.	197170403	197170772	0	2	1,1	0,368	3.49705	20.24510	18.84326
ERROR: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	197067496	197068289	Peak_280961	9	.	197067496	197068289	0	1	793	0	1.14222	1.81522	0.92546
ERROR: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	197138856	197139464	Peak_370837	0	.	197138856	197139464	0	2	150,1	0,607	1.17258	0.95909	0.04879

Num	58
ID	task.idr.idr2_rep1_rep2.line_72.id_63
Name	idr2 rep1-rep2
Thread	thread_Root
PID	44765

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

Start	2016-05-17 17:16:41
End	2016-05-17 17:25:30
Elapsed	00:08:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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 - 389366/389366 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 182894/389366 (47.0%)

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3045752	3046586	.	843	.	1.39898	5.13569	3.31838	181	1.71	2.03	0

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3045752	3046586	.	843	.	1.39898	5.13569	3.31838	181	1.71	2.03	0

Num	59
ID	task.idr.idr2_rep1_pr.line_72.id_64
Name	idr2 rep1-pr
Thread	thread_Root
PID	44774

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

Start	2016-05-17 17:16:41
End	2016-05-17 17:23:48
Elapsed	00:07:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt.png /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 90

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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 0.86 0.38]
Number of reported peaks - 376549/376549 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 190172/376549 (50.5%)

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	.	426	.	1.47097	3.57908	1.74302	1004	0.30	1.03	0

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	.	426	.	1.47097	3.57908	1.74302	1004	0.30	1.03	0

Num	60
ID	task.idr.idr2_rep2_pr.line_72.id_65
Name	idr2 rep2-pr
Thread	thread_Root
PID	44785

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

Start	2016-05-17 17:16:42
End	2016-05-17 17:22:59
Elapsed	00:06:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt.png /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 90

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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 - 365577/365577 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 194222/365577 (53.1%)

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr5	109983658	109984119	.	711	.	1.43587	3.75154	1.88310	68	1.05	1.71	0

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr5	109983658	109984119	.	711	.	1.43587	3.75154	1.88310	68	1.05	1.71	0

Num	61
ID	task.idr.idr2_ppr.line_72.id_66
Name	idr2 ppr
Thread	thread_Root
PID	44800

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

Start	2016-05-17 17:16:42
End	2016-05-17 17:24:40
Elapsed	00:07:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt.png /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz

# SYS command. line 86

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.narrowPeak.gz

# SYS command. line 87

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 90

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 91

 zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.12-col.bed.gz

# SYS command. line 93

 gzip -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.unthresholded-peaks.txt

# SYS command. line 94

 rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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 - 415213/415213 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 252678/415213 (60.9%)

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3045752	3046586	.	1000	.	1.39898	5.13569	3.31838	181	2.88	3.25	0

***** WARNING: File /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.13-col.bed.gz has inconsistent naming convention for record:
mm9_chr11	3045752	3046586	.	1000	.	1.39898	5.13569	3.31838	181	2.88	3.25	0

Num	62
ID	task.base.line_414.id_75
Name	task.base.line_414.id_75
Thread	thread_Root
PID	48585

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

Start	2016-05-17 17:25:31
End	2016-05-17 17:25:31
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	48590

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

Start	2016-05-17 17:25:31
End	2016-05-17 17:25:31
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	48598

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

Start	2016-05-17 17:25:31
End	2016-05-17 17:25:31
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.12-col.bed.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.12-col.bed.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.12-col.bed.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	48610

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

Start	2016-05-17 17:25:31
End	2016-05-17 17:25:31
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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	48634

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

Start	2016-05-17 17:25:32
End	2016-05-17 17:25:33
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep1/rep1-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pseudo_reps/rep2/rep2-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/IDR_final.qc

# SYS command. line 215

 echo -e "183800\t190651	194671	""253106\trep1-rep2\tpooled_pseudo_rep\t1.3770729053318824\t1.0210856486459552\t1" >> /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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.postalign_bam.srt_bam_rep1.line_345.id_80
Name	srt_bam rep1
Thread	thread_136
PID	48639

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

Start	2016-05-17 17:25:32
End	2016-05-17 18:12:28
Elapsed	00:46:56
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bam
Dependencies

 
# SYS command. line 347

 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 353

 samtools sort /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bam.bai /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bai; \
			fi

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 60 files...

Num	68
ID	task.postalign_bam.srt_bam_rep2.line_345.id_81
Name	srt_bam rep2
Thread	thread_137
PID	48647

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

Start	2016-05-17 17:25:32
End	2016-05-17 18:47:38
Elapsed	01:22:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bam
Dependencies

 
# SYS command. line 347

 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 353

 samtools sort /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bam.bai /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bai; \
			fi

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 95 files...

Num	69
ID	task.atac.ataqc_rep1.line_847.id_82
Name	ataqc rep1
Thread	thread_136
PID	15669

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

Start	2016-05-17 18:12:29
End	2016-05-17 18:12:29
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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE_qc.html /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE_qc.txt
Dependencies

 
# SYS command. line 849

 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 853

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

# SYS command. line 855

 cd /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1

# SYS command. line 857

 /srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1 \
			    --outdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
			    --naive_overlap_peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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	70
ID	task.atac.ataqc_rep2.line_847.id_83
Name	ataqc rep2
Thread	thread_137
PID	27512

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

Start	2016-05-17 18:47:39
End	2016-05-17 18:47:39
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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE_qc.html /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE_qc.txt
Dependencies

 
# SYS command. line 849

 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 853

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

# SYS command. line 855

 cd /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2

# SYS command. line 857

 /srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2 \
			    --outdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
			    --naive_overlap_peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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/stemcells/het/output/4x_experiments/UnplacedChroms_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, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_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_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq]
string	BASSETDIR	/srv/scratch/annashch/Basset
bool	canFail	false
int	cpus	1
int	cpusLocal	48
string	CRC	/srv/scratch/annashch/crc
int	day	86400
string	DEEPLEARN_SCRIPTS_DIR	/srv/scratch/annashch/deeplearning_avanti
string	DEEPLIFT_DIR	/srv/scratch/annashch/deeplift/deeplift
real	E	2.718281828459045
string	EIGEN	/mnt/lab_data/montgomery/shared/Eigen
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/annashch/enhancer_prediction_code
int	G	1073741824
string	HOME	/users/annashch/
int	hour	3600
int	K	1024
string	KERAS_DIR	/users/annashch/keras
string	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
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

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