| Num | 1 | | ID | task.callpeak_macs2.macs2_atac_rep1.line_192.id_6 | | Name | macs2_atac rep1 | | Thread | thread_20 | | PID | 25080 | | | OK | false | | Exit Code | 0 | | Retries | | | State | RUNNING | | Dep. | WAIT | | Cpus | 2 | | Mem | | | | Start | 2016-05-18 00:39:00 | | End | 2016-05-18 00:39:00 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
| | Output files | /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz
/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig
/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_summits.bed
# SYS command. line 217
if [[ true == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO @ Wed, 18 May 2016 00:39:03:
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Wed, 18 May 2016 00:39:03: #1 read tag files...
INFO @ Wed, 18 May 2016 00:39:03: #1 read treatment tags...
INFO @ Wed, 18 May 2016 00:39:05: 1000000
INFO @ Wed, 18 May 2016 00:39:07: 2000000
INFO @ Wed, 18 May 2016 00:39:09: 3000000
INFO @ Wed, 18 May 2016 00:39:11: 4000000
INFO @ Wed, 18 May 2016 00:39:13: 5000000
INFO @ Wed, 18 May 2016 00:39:15: 6000000
INFO @ Wed, 18 May 2016 00:39:17: 7000000
INFO @ Wed, 18 May 2016 00:39:19: 8000000
INFO @ Wed, 18 May 2016 00:39:21: 9000000
INFO @ Wed, 18 May 2016 00:39:23: 10000000
INFO @ Wed, 18 May 2016 00:39:25: 11000000
INFO @ Wed, 18 May 2016 00:39:27: 12000000
INFO @ Wed, 18 May 2016 00:39:29: 13000000
INFO @ Wed, 18 May 2016 00:39:31: 14000000
INFO @ Wed, 18 May 2016 00:39:33: 15000000
INFO @ Wed, 18 May 2016 00:39:35: 16000000
INFO @ Wed, 18 May 2016 00:39:37: 17000000
INFO @ Wed, 18 May 2016 00:39:39: 18000000
INFO @ Wed, 18 May 2016 00:39:40: 19000000
INFO @ Wed, 18 May 2016 00:39:42: 20000000
INFO @ Wed, 18 May 2016 00:39:44: 21000000
INFO @ Wed, 18 May 2016 00:39:46: 22000000
INFO @ Wed, 18 May 2016 00:39:48: 23000000
INFO @ Wed, 18 May 2016 00:39:50: 24000000
INFO @ Wed, 18 May 2016 00:39:52: 25000000
INFO @ Wed, 18 May 2016 00:39:54: 26000000
INFO @ Wed, 18 May 2016 00:39:56: 27000000
INFO @ Wed, 18 May 2016 00:39:58: 28000000
INFO @ Wed, 18 May 2016 00:40:00: 29000000
INFO @ Wed, 18 May 2016 00:40:02: 30000000
INFO @ Wed, 18 May 2016 00:40:04: 31000000
INFO @ Wed, 18 May 2016 00:40:06: 32000000
INFO @ Wed, 18 May 2016 00:40:08: 33000000
INFO @ Wed, 18 May 2016 00:40:10: 34000000
INFO @ Wed, 18 May 2016 00:40:12: 35000000
INFO @ Wed, 18 May 2016 00:40:14: 36000000
INFO @ Wed, 18 May 2016 00:40:16: 37000000
INFO @ Wed, 18 May 2016 00:40:18: 38000000
INFO @ Wed, 18 May 2016 00:40:20: 39000000
INFO @ Wed, 18 May 2016 00:40:22: 40000000
INFO @ Wed, 18 May 2016 00:40:24: 41000000
INFO @ Wed, 18 May 2016 00:40:26: 42000000
INFO @ Wed, 18 May 2016 00:40:28: 43000000
INFO @ Wed, 18 May 2016 00:40:30: 44000000
INFO @ Wed, 18 May 2016 00:40:32: 45000000
INFO @ Wed, 18 May 2016 00:40:34: 46000000
INFO @ Wed, 18 May 2016 00:40:36: 47000000
INFO @ Wed, 18 May 2016 00:40:38: 48000000
INFO @ Wed, 18 May 2016 00:40:40: 49000000
INFO @ Wed, 18 May 2016 00:40:42: 50000000
INFO @ Wed, 18 May 2016 00:40:44: 51000000
INFO @ Wed, 18 May 2016 00:40:46: 52000000
INFO @ Wed, 18 May 2016 00:40:53: #1 tag size is determined as 67 bps
INFO @ Wed, 18 May 2016 00:40:53: #1 tag size = 67
INFO @ Wed, 18 May 2016 00:40:53: #1 total tags in treatment: 52989484
INFO @ Wed, 18 May 2016 00:40:53: #1 finished!
INFO @ Wed, 18 May 2016 00:40:53: #2 Build Peak Model...
INFO @ Wed, 18 May 2016 00:40:53: #2 Skipped...
INFO @ Wed, 18 May 2016 00:40:53: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Wed, 18 May 2016 00:40:53: #2 Use 150 as fragment length
INFO @ Wed, 18 May 2016 00:40:53: #3 Call peaks...
INFO @ Wed, 18 May 2016 00:40:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Wed, 18 May 2016 00:40:53: #3 Pre-compute pvalue-qvalue table...
|
| Num | 2 | | ID | task.callpeak_macs2.macs2_atac_rep2_pr1.pval0.1.line_192.id_7 | | Name | macs2_atac rep2-pr1.pval0.1 | | Thread | thread_21 | | PID | 25085 | | | OK | false | | Exit Code | 0 | | Retries | | | State | RUNNING | | Dep. | WAIT | | Cpus | 2 | | Mem | | | | Start | 2016-05-18 00:39:00 | | End | 2016-05-18 00:39:00 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/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_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz
/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_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_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_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_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/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_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/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_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO @ Wed, 18 May 2016 00:39:03:
# Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_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_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Wed, 18 May 2016 00:39:03: #1 read tag files...
INFO @ Wed, 18 May 2016 00:39:03: #1 read treatment tags...
INFO @ Wed, 18 May 2016 00:39:06: 1000000
INFO @ Wed, 18 May 2016 00:39:08: 2000000
INFO @ Wed, 18 May 2016 00:39:10: 3000000
INFO @ Wed, 18 May 2016 00:39:12: 4000000
INFO @ Wed, 18 May 2016 00:39:14: 5000000
INFO @ Wed, 18 May 2016 00:39:16: 6000000
INFO @ Wed, 18 May 2016 00:39:18: 7000000
INFO @ Wed, 18 May 2016 00:39:20: 8000000
INFO @ Wed, 18 May 2016 00:39:22: 9000000
INFO @ Wed, 18 May 2016 00:39:24: 10000000
INFO @ Wed, 18 May 2016 00:39:26: 11000000
INFO @ Wed, 18 May 2016 00:39:28: 12000000
INFO @ Wed, 18 May 2016 00:39:30: 13000000
INFO @ Wed, 18 May 2016 00:39:32: 14000000
INFO @ Wed, 18 May 2016 00:39:34: 15000000
INFO @ Wed, 18 May 2016 00:39:36: 16000000
INFO @ Wed, 18 May 2016 00:39:38: 17000000
INFO @ Wed, 18 May 2016 00:39:40: 18000000
INFO @ Wed, 18 May 2016 00:39:42: 19000000
INFO @ Wed, 18 May 2016 00:39:44: 20000000
INFO @ Wed, 18 May 2016 00:39:46: 21000000
INFO @ Wed, 18 May 2016 00:39:48: 22000000
INFO @ Wed, 18 May 2016 00:39:50: 23000000
INFO @ Wed, 18 May 2016 00:39:52: 24000000
INFO @ Wed, 18 May 2016 00:39:54: 25000000
INFO @ Wed, 18 May 2016 00:39:57: #1 tag size is determined as 70 bps
INFO @ Wed, 18 May 2016 00:39:57: #1 tag size = 70
INFO @ Wed, 18 May 2016 00:39:57: #1 total tags in treatment: 25509324
INFO @ Wed, 18 May 2016 00:39:57: #1 finished!
INFO @ Wed, 18 May 2016 00:39:57: #2 Build Peak Model...
INFO @ Wed, 18 May 2016 00:39:57: #2 Skipped...
INFO @ Wed, 18 May 2016 00:39:57: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Wed, 18 May 2016 00:39:57: #2 Use 150 as fragment length
INFO @ Wed, 18 May 2016 00:39:57: #3 Call peaks...
INFO @ Wed, 18 May 2016 00:39:57: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000...
INFO @ Wed, 18 May 2016 00:39:57: #3 Pre-compute pvalue-qvalue table...
INFO @ Wed, 18 May 2016 00:41:18: #3 Call peaks for each chromosome...
INFO @ Wed, 18 May 2016 00:42:59: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls
INFO @ Wed, 18 May 2016 00:43:02: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak
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