Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
Num | 1 | ID | task.idr.idr2_rep1_rep2.line_61.id_6 | Name | idr2 rep1-rep2 | Thread | thread_Root | PID | 130023 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:16:36 | End | 2016-05-16 20:20:48 | Elapsed | 00:04:11 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| Dependencies | | |
# SYS command. line 63
if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 65
idr --samples /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
--plot --use-best-multisummit-IDR
# SYS command. line 69
idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 72
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz
# SYS command. line 75
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz
# SYS command. line 78
bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz; bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/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/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
# SYS command. line 80
gzip -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.76 0.75 0.78 0.31]
/users/pangwei/anaconda3/envs/bds_atac_py3/lib/python3.5/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
/users/pangwei/anaconda3/envs/bds_atac_py3/lib/python3.5/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
Number of reported peaks - 210642/210642 (100.0%)
Number of peaks passing IDR cutoff of 0.1 - 83055/210642 (39.4%)
|
Num | 2 | ID | task.base.line_414.id_9 | Name | task.base.line_414.id_9 | Thread | thread_Root | PID | 130952 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:20:48 | End | 2016-05-16 20:20:49 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
|
Num | 3 | ID | task.base.line_414.id_10 | Name | task.base.line_414.id_10 | Thread | thread_Root | PID | 130959 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:20:48 | End | 2016-05-16 20:20:49 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
|
Num | 4 | ID | task.base.line_414.id_11 | Name | task.base.line_414.id_11 | Thread | thread_Root | PID | 130969 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:20:48 | End | 2016-05-16 20:20:49 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
|
Num | 5 | ID | task.base.line_414.id_12 | Name | task.base.line_414.id_12 | Thread | thread_Root | PID | 130983 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:20:49 | End | 2016-05-16 20:20:49 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
|
Num | 6 | ID | task.idr.idr_final_qc.line_196.id_13 | Name | idr final qc | Thread | thread_Root | PID | 131001 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:20:49 | End | 2016-05-16 20:20:50 | Elapsed | 00:00:01 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/IDR_final.qc
| Dependencies | | |
# SYS command. line 198
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 200
echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/IDR_final.qc
# SYS command. line 201
echo -e "83109\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/IDR_final.qc
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
Num | 7 | ID | task.postalign_bam.srt_bam_rep1.line_345.id_14 | Name | srt_bam rep1 | Thread | thread_36 | PID | 131008 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:20:49 | End | 2016-05-16 20:51:24 | Elapsed | 00:30:34 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt.bam
| Dependencies | | |
# SYS command. line 347
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 353
samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt
# SYS command. line 354
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt.bam
# SYS command. line 356
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt.bai; \
fi
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 39 files...
|
Num | 8 | ID | task.postalign_bam.srt_bam_rep2.line_345.id_15 | Name | srt_bam rep2 | Thread | thread_37 | PID | 131020 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:20:50 | End | 2016-05-16 21:24:18 | Elapsed | 01:03:28 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt.bam
| Dependencies | | |
# SYS command. line 347
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 353
samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt
# SYS command. line 354
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt.bam
# SYS command. line 356
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt.bai; \
fi
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 79 files...
|
Num | 9 | ID | task.atac.ataqc_rep1.line_815.id_16 | Name | ataqc rep1 | Thread | thread_36 | PID | 132805 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 20:51:25 | End | 2016-05-16 22:49:54 | Elapsed | 01:58:29 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair2.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.align.log
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.PE2SE_qc.html
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.PE2SE_qc.txt
| Dependencies | | |
# SYS command. line 817
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 821
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 823
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1
# SYS command. line 825
/users/pangwei/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1 \
--outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1 \
--outprefix ATAC9-trimmed-pair1.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/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair2.fastq.gz \
--alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
--bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
\
--idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
--------------------Stdout--------------------
Run time: 1:58:27
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR 2016-05-16 20:55:26 ProcessExecutor Warning messages:
ERROR 2016-05-16 20:55:26 ProcessExecutor 1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-16 20:55:26 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-16 20:55:26 ProcessExecutor 2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-16 20:55:26 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-16 20:55:26 ProcessExecutor 3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-16 20:55:26 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-16 20:55:26 ProcessExecutor 4: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-16 20:55:26 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 40 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
sorted_results = merged.sort('corr', ascending=True)
|
Num | 10 | ID | task.atac.ataqc_rep2.line_815.id_17 | Name | ataqc rep2 | Thread | thread_37 | PID | 133744 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 21:24:19 | End | 2016-05-17 01:14:18 | Elapsed | 03:49:58 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair2.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.align.log
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.PE2SE_qc.html
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.PE2SE_qc.txt
| Dependencies | | |
# SYS command. line 817
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 821
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 823
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2
# SYS command. line 825
/users/pangwei/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2 \
--outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2 \
--outprefix ATAC10-trimmed-pair1.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/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair2.fastq.gz \
--alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
--bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
\
--idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
--------------------Stdout--------------------
Run time: 3:49:55
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR 2016-05-16 21:29:31 ProcessExecutor Warning messages:
ERROR 2016-05-16 21:29:31 ProcessExecutor 1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-16 21:29:31 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-16 21:29:31 ProcessExecutor 2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-16 21:29:31 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 80 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Could not delete file /tmp/pangwei/sortingcollection.7098419587720231130.tmp
Could not delete file /tmp/pangwei/sortingcollection.2481812707648940260.tmp
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
sorted_results = merged.sort('corr', ascending=True)
|
Num | 11 | ID | task.report.line_418.id_18 | Name | task.report.line_418.id_18 | Thread | thread_Root | PID | 141161 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-17 01:14:22 | End | 2016-05-17 01:14:28 | Elapsed | 00:00:06 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock.gz
| Dependencies | | |
# SYS command. line 420
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 421
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp
# SYS command. line 423
/users/pangwei/bds_atac/utils/narrowpeak_idr.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock
# SYS command. line 424
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
Num | 12 | ID | task.report.line_418.id_19 | Name | task.report.line_418.id_19 | Thread | thread_Root | PID | 141234 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-17 01:14:29 | End | 2016-05-17 01:14:37 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
| Dependencies | | |
# SYS command. line 420
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 421
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
# SYS command. line 423
/users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock
# SYS command. line 424
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
Num | 13 | ID | task.report.line_418.id_20 | Name | task.report.line_418.id_20 | Thread | thread_Root | PID | 141326 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-17 01:14:38 | End | 2016-05-17 01:14:48 | Elapsed | 00:00:09 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
| Dependencies | | |
# SYS command. line 420
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 421
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
# SYS command. line 423
/users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock
# SYS command. line 424
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
Num | 14 | ID | task.report_graphviz.line_93.id_21 | Name | task.report_graphviz.line_93.id_21 | Thread | thread_Root | PID | 141434 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-17 01:14:49 | End | 2016-05-17 01:14:53 | Elapsed | 00:00:04 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | | Output files | | Dependencies | | |
# SYS command. line 94
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 95
dot -Tsvg /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/report/workflow.dot > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/report/workflow.svg
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
Num | 15 | ID | task.report.line_383.id_26 | Name | task.report.line_383.id_26 | Thread | thread_Root | PID | 141438 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-17 01:14:49 | End | 2016-05-17 01:14:53 | Elapsed | 00:00:04 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | | Output files | | Dependencies | | |
# SYS command. line 384
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 385
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
Num | 16 | ID | task.report.line_383.id_27 | Name | task.report.line_383.id_27 | Thread | thread_Root | PID | 141440 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-17 01:14:49 | End | 2016-05-17 01:14:53 | Elapsed | 00:00:04 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | | Output files | | Dependencies | | |
# SYS command. line 384
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 385
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
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