Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
Num | 1 | ID | task.postalign_bed.xcor_rep2.line_212.id_10 | Name | xcor rep2 | Thread | thread_42 | PID | 47037 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 2 | Mem | | | Start | 2017-04-13 22:05:54 | End | 2017-04-13 22:17:52 | Elapsed | 00:11:58 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf
| Dependencies | | |
# SYS command. line 214
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz -p=2 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
27559 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 2
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.15M.tagAlign.gz
opened /tmp/47037.1.q/Rtmpi2D0IR/ENCFF241VRG.15M.tagAlign6c5f3f1cefef
done. read 15000000 fragments
ChIP data read length 101
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1658969
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.250439643923327,0.25042833670953
Top 3 estimates for fragment length 240,250
Window half size 615
Phantom peak location 105
Phantom peak Correlation 0.2242136
Normalized Strand cross-correlation coefficient (NSC) 1.50961
Relative Strand cross-correlation Coefficient (RSC) 1.449716
Phantom Peak Quality Tag 1
null device
1
--------------------Stderr--------------------
Loading required package: caTools
|
Num | 2 | ID | task.postalign_bed.xcor_rep1.line_212.id_11 | Name | xcor rep1 | Thread | thread_41 | PID | 47038 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 2 | Mem | | | Start | 2017-04-13 22:05:54 | End | 2017-04-13 22:17:57 | Elapsed | 00:12:03 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf
| Dependencies | | |
# SYS command. line 214
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz -p=2 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
27560 (process ID) old priority 0, new priority 19
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 2
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.15M.tagAlign.gz
opened /tmp/47038.1.q/RtmpIAI1IR/ENCFF066ZSK.15M.tagAlign6c676c6c4cc2
done. read 15000000 fragments
ChIP data read length 101
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.167174
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.246658462691947
Top 3 estimates for fragment length 235
Window half size 630
Phantom peak location 105
Phantom peak Correlation 0.2228084
Normalized Strand cross-correlation coefficient (NSC) 1.475459
Relative Strand cross-correlation Coefficient (RSC) 1.428692
Phantom Peak Quality Tag 1
null device
1
--------------------Stderr--------------------
Loading required package: caTools
|
Num | 3 | ID | task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_12 | Name | macs2 n/s pooled_rep | Thread | thread_Root | PID | 47039 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:18:02 | End | 2017-04-14 01:55:27 | Elapsed | 03:37:24 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep -o "ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep -o "ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
26841 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:18:17:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:18:17: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:18:17: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:18:19: 1000000
INFO @ Thu, 13 Apr 2017 22:18:21: 2000000
INFO @ Thu, 13 Apr 2017 22:18:22: 3000000
INFO @ Thu, 13 Apr 2017 22:18:24: 4000000
INFO @ Thu, 13 Apr 2017 22:18:26: 5000000
INFO @ Thu, 13 Apr 2017 22:18:28: 6000000
INFO @ Thu, 13 Apr 2017 22:18:30: 7000000
INFO @ Thu, 13 Apr 2017 22:18:32: 8000000
INFO @ Thu, 13 Apr 2017 22:18:33: 9000000
INFO @ Thu, 13 Apr 2017 22:18:35: 10000000
INFO @ Thu, 13 Apr 2017 22:18:37: 11000000
INFO @ Thu, 13 Apr 2017 22:18:38: 12000000
INFO @ Thu, 13 Apr 2017 22:18:40: 13000000
INFO @ Thu, 13 Apr 2017 22:18:42: 14000000
INFO @ Thu, 13 Apr 2017 22:18:43: 15000000
INFO @ Thu, 13 Apr 2017 22:18:45: 16000000
INFO @ Thu, 13 Apr 2017 22:18:47: 17000000
INFO @ Thu, 13 Apr 2017 22:18:48: 18000000
INFO @ Thu, 13 Apr 2017 22:18:50: 19000000
INFO @ Thu, 13 Apr 2017 22:18:52: 20000000
INFO @ Thu, 13 Apr 2017 22:18:53: 21000000
INFO @ Thu, 13 Apr 2017 22:18:55: 22000000
INFO @ Thu, 13 Apr 2017 22:18:57: 23000000
INFO @ Thu, 13 Apr 2017 22:18:58: 24000000
INFO @ Thu, 13 Apr 2017 22:19:00: 25000000
INFO @ Thu, 13 Apr 2017 22:19:02: 26000000
INFO @ Thu, 13 Apr 2017 22:19:03: 27000000
INFO @ Thu, 13 Apr 2017 22:19:05: 28000000
INFO @ Thu, 13 Apr 2017 22:19:07: 29000000
INFO @ Thu, 13 Apr 2017 22:19:08: 30000000
INFO @ Thu, 13 Apr 2017 22:19:10: 31000000
INFO @ Thu, 13 Apr 2017 22:19:12: 32000000
INFO @ Thu, 13 Apr 2017 22:19:13: 33000000
INFO @ Thu, 13 Apr 2017 22:19:15: 34000000
INFO @ Thu, 13 Apr 2017 22:19:17: 35000000
INFO @ Thu, 13 Apr 2017 22:19:18: 36000000
INFO @ Thu, 13 Apr 2017 22:19:20: 37000000
INFO @ Thu, 13 Apr 2017 22:19:22: 38000000
INFO @ Thu, 13 Apr 2017 22:19:23: 39000000
INFO @ Thu, 13 Apr 2017 22:19:25: 40000000
INFO @ Thu, 13 Apr 2017 22:19:27: 41000000
INFO @ Thu, 13 Apr 2017 22:19:28: 42000000
INFO @ Thu, 13 Apr 2017 22:19:30: 43000000
INFO @ Thu, 13 Apr 2017 22:19:32: 44000000
INFO @ Thu, 13 Apr 2017 22:19:33: 45000000
INFO @ Thu, 13 Apr 2017 22:19:35: 46000000
INFO @ Thu, 13 Apr 2017 22:19:37: 47000000
INFO @ Thu, 13 Apr 2017 22:19:38: 48000000
INFO @ Thu, 13 Apr 2017 22:19:40: 49000000
INFO @ Thu, 13 Apr 2017 22:19:42: 50000000
INFO @ Thu, 13 Apr 2017 22:19:43: 51000000
INFO @ Thu, 13 Apr 2017 22:19:45: 52000000
INFO @ Thu, 13 Apr 2017 22:19:47: 53000000
INFO @ Thu, 13 Apr 2017 22:19:48: 54000000
INFO @ Thu, 13 Apr 2017 22:19:50: 55000000
INFO @ Thu, 13 Apr 2017 22:19:52: 56000000
INFO @ Thu, 13 Apr 2017 22:19:53: 57000000
INFO @ Thu, 13 Apr 2017 22:19:55: 58000000
INFO @ Thu, 13 Apr 2017 22:19:57: 59000000
INFO @ Thu, 13 Apr 2017 22:19:58: 60000000
INFO @ Thu, 13 Apr 2017 22:20:00: 61000000
INFO @ Thu, 13 Apr 2017 22:20:02: 62000000
INFO @ Thu, 13 Apr 2017 22:20:03: 63000000
INFO @ Thu, 13 Apr 2017 22:20:05: 64000000
INFO @ Thu, 13 Apr 2017 22:20:07: 65000000
INFO @ Thu, 13 Apr 2017 22:20:08: 66000000
INFO @ Thu, 13 Apr 2017 22:20:10: 67000000
INFO @ Thu, 13 Apr 2017 22:20:12: 68000000
INFO @ Thu, 13 Apr 2017 22:20:13: 69000000
INFO @ Thu, 13 Apr 2017 22:20:15: 70000000
INFO @ Thu, 13 Apr 2017 22:20:17: 71000000
INFO @ Thu, 13 Apr 2017 22:20:18: 72000000
INFO @ Thu, 13 Apr 2017 22:20:20: 73000000
INFO @ Thu, 13 Apr 2017 22:20:22: 74000000
INFO @ Thu, 13 Apr 2017 22:20:24: 75000000
INFO @ Thu, 13 Apr 2017 22:20:25: 76000000
INFO @ Thu, 13 Apr 2017 22:20:27: 77000000
INFO @ Thu, 13 Apr 2017 22:20:28: 78000000
INFO @ Thu, 13 Apr 2017 22:20:30: 79000000
INFO @ Thu, 13 Apr 2017 22:20:32: 80000000
INFO @ Thu, 13 Apr 2017 22:20:33: 81000000
INFO @ Thu, 13 Apr 2017 22:20:35: 82000000
INFO @ Thu, 13 Apr 2017 22:20:37: 83000000
INFO @ Thu, 13 Apr 2017 22:20:38: 84000000
INFO @ Thu, 13 Apr 2017 22:20:40: 85000000
INFO @ Thu, 13 Apr 2017 22:20:42: 86000000
INFO @ Thu, 13 Apr 2017 22:20:43: 87000000
INFO @ Thu, 13 Apr 2017 22:20:45: 88000000
INFO @ Thu, 13 Apr 2017 22:20:47: 89000000
INFO @ Thu, 13 Apr 2017 22:20:49: 90000000
INFO @ Thu, 13 Apr 2017 22:20:50: 91000000
INFO @ Thu, 13 Apr 2017 22:20:52: 92000000
INFO @ Thu, 13 Apr 2017 22:20:54: 93000000
INFO @ Thu, 13 Apr 2017 22:20:55: 94000000
INFO @ Thu, 13 Apr 2017 22:20:57: 95000000
INFO @ Thu, 13 Apr 2017 22:20:59: 96000000
INFO @ Thu, 13 Apr 2017 22:21:00: 97000000
INFO @ Thu, 13 Apr 2017 22:21:02: 98000000
INFO @ Thu, 13 Apr 2017 22:21:03: 99000000
INFO @ Thu, 13 Apr 2017 22:21:05: 100000000
INFO @ Thu, 13 Apr 2017 22:21:07: 101000000
INFO @ Thu, 13 Apr 2017 22:21:08: 102000000
INFO @ Thu, 13 Apr 2017 22:21:10: 103000000
INFO @ Thu, 13 Apr 2017 22:21:12: 104000000
INFO @ Thu, 13 Apr 2017 22:21:13: 105000000
INFO @ Thu, 13 Apr 2017 22:21:15: 106000000
INFO @ Thu, 13 Apr 2017 22:21:17: 107000000
INFO @ Thu, 13 Apr 2017 22:21:18: 108000000
INFO @ Thu, 13 Apr 2017 22:21:20: 109000000
INFO @ Thu, 13 Apr 2017 22:21:22: 110000000
INFO @ Thu, 13 Apr 2017 22:21:23: 111000000
INFO @ Thu, 13 Apr 2017 22:21:25: 112000000
INFO @ Thu, 13 Apr 2017 22:21:27: 113000000
INFO @ Thu, 13 Apr 2017 22:21:29: 114000000
INFO @ Thu, 13 Apr 2017 22:21:30: 115000000
INFO @ Thu, 13 Apr 2017 22:21:32: 116000000
INFO @ Thu, 13 Apr 2017 22:21:34: 117000000
INFO @ Thu, 13 Apr 2017 22:21:35: 118000000
INFO @ Thu, 13 Apr 2017 22:21:37: 119000000
INFO @ Thu, 13 Apr 2017 22:21:38: 120000000
INFO @ Thu, 13 Apr 2017 22:21:40: 121000000
INFO @ Thu, 13 Apr 2017 22:21:42: 122000000
INFO @ Thu, 13 Apr 2017 22:21:43: 123000000
INFO @ Thu, 13 Apr 2017 22:21:45: 124000000
INFO @ Thu, 13 Apr 2017 22:21:47: 125000000
INFO @ Thu, 13 Apr 2017 22:21:48: 126000000
INFO @ Thu, 13 Apr 2017 22:21:50: 127000000
INFO @ Thu, 13 Apr 2017 22:21:52: 128000000
INFO @ Thu, 13 Apr 2017 22:21:53: 129000000
INFO @ Thu, 13 Apr 2017 22:21:55: 130000000
INFO @ Thu, 13 Apr 2017 22:21:57: 131000000
INFO @ Thu, 13 Apr 2017 22:21:58: 132000000
INFO @ Thu, 13 Apr 2017 22:22:00: 133000000
INFO @ Thu, 13 Apr 2017 22:22:02: 134000000
INFO @ Thu, 13 Apr 2017 22:22:03: 135000000
INFO @ Thu, 13 Apr 2017 22:22:05: 136000000
INFO @ Thu, 13 Apr 2017 22:22:07: 137000000
INFO @ Thu, 13 Apr 2017 22:22:08: 138000000
INFO @ Thu, 13 Apr 2017 22:22:10: 139000000
INFO @ Thu, 13 Apr 2017 22:22:12: 140000000
INFO @ Thu, 13 Apr 2017 22:22:13: 141000000
INFO @ Thu, 13 Apr 2017 22:22:15: 142000000
INFO @ Thu, 13 Apr 2017 22:22:17: 143000000
INFO @ Thu, 13 Apr 2017 22:22:18: 144000000
INFO @ Thu, 13 Apr 2017 22:22:20: 145000000
INFO @ Thu, 13 Apr 2017 22:22:22: 146000000
INFO @ Thu, 13 Apr 2017 22:22:24: 147000000
INFO @ Thu, 13 Apr 2017 22:22:25: 148000000
INFO @ Thu, 13 Apr 2017 22:22:27: 149000000
INFO @ Thu, 13 Apr 2017 22:22:29: 150000000
INFO @ Thu, 13 Apr 2017 22:22:30: 151000000
INFO @ Thu, 13 Apr 2017 22:22:32: 152000000
INFO @ Thu, 13 Apr 2017 22:22:34: 153000000
INFO @ Thu, 13 Apr 2017 22:22:35: 154000000
INFO @ Thu, 13 Apr 2017 22:22:37: 155000000
INFO @ Thu, 13 Apr 2017 22:22:39: 156000000
INFO @ Thu, 13 Apr 2017 22:22:40: 157000000
INFO @ Thu, 13 Apr 2017 22:22:42: 158000000
INFO @ Thu, 13 Apr 2017 22:22:44: 159000000
INFO @ Thu, 13 Apr 2017 22:22:45: 160000000
INFO @ Thu, 13 Apr 2017 22:22:47: 161000000
INFO @ Thu, 13 Apr 2017 22:22:49: 162000000
INFO @ Thu, 13 Apr 2017 22:22:50: 163000000
INFO @ Thu, 13 Apr 2017 22:22:52: 164000000
INFO @ Thu, 13 Apr 2017 22:22:54: 165000000
INFO @ Thu, 13 Apr 2017 22:22:55: 166000000
INFO @ Thu, 13 Apr 2017 22:22:57: 167000000
INFO @ Thu, 13 Apr 2017 22:22:59: 168000000
INFO @ Thu, 13 Apr 2017 22:23:00: 169000000
INFO @ Thu, 13 Apr 2017 22:23:02: 170000000
INFO @ Thu, 13 Apr 2017 22:23:04: 171000000
INFO @ Thu, 13 Apr 2017 22:23:05: 172000000
INFO @ Thu, 13 Apr 2017 22:23:07: 173000000
INFO @ Thu, 13 Apr 2017 22:23:09: 174000000
INFO @ Thu, 13 Apr 2017 22:23:10: 175000000
INFO @ Thu, 13 Apr 2017 22:23:12: 176000000
INFO @ Thu, 13 Apr 2017 22:23:14: 177000000
INFO @ Thu, 13 Apr 2017 22:23:15: 178000000
INFO @ Thu, 13 Apr 2017 22:23:17: 179000000
INFO @ Thu, 13 Apr 2017 22:23:19: 180000000
INFO @ Thu, 13 Apr 2017 22:23:21: 181000000
INFO @ Thu, 13 Apr 2017 22:23:22: 182000000
INFO @ Thu, 13 Apr 2017 22:23:24: 183000000
INFO @ Thu, 13 Apr 2017 22:23:26: 184000000
INFO @ Thu, 13 Apr 2017 22:23:27: 185000000
INFO @ Thu, 13 Apr 2017 22:23:29: 186000000
INFO @ Thu, 13 Apr 2017 22:23:31: 187000000
INFO @ Thu, 13 Apr 2017 22:23:32: 188000000
INFO @ Thu, 13 Apr 2017 22:23:34: 189000000
INFO @ Thu, 13 Apr 2017 22:23:36: 190000000
INFO @ Thu, 13 Apr 2017 22:23:37: 191000000
INFO @ Thu, 13 Apr 2017 22:23:39: 192000000
INFO @ Thu, 13 Apr 2017 22:23:40: 193000000
INFO @ Thu, 13 Apr 2017 22:23:42: 194000000
INFO @ Thu, 13 Apr 2017 22:23:44: 195000000
INFO @ Thu, 13 Apr 2017 22:23:46: 196000000
INFO @ Thu, 13 Apr 2017 22:23:47: 197000000
INFO @ Thu, 13 Apr 2017 22:23:49: 198000000
INFO @ Thu, 13 Apr 2017 22:23:50: 199000000
INFO @ Thu, 13 Apr 2017 22:23:52: 200000000
INFO @ Thu, 13 Apr 2017 22:23:54: 201000000
INFO @ Thu, 13 Apr 2017 22:23:55: 202000000
INFO @ Thu, 13 Apr 2017 22:23:57: 203000000
INFO @ Thu, 13 Apr 2017 22:23:59: 204000000
INFO @ Thu, 13 Apr 2017 22:24:00: 205000000
INFO @ Thu, 13 Apr 2017 22:24:02: 206000000
INFO @ Thu, 13 Apr 2017 22:24:04: 207000000
INFO @ Thu, 13 Apr 2017 22:24:05: 208000000
INFO @ Thu, 13 Apr 2017 22:24:07: 209000000
INFO @ Thu, 13 Apr 2017 22:24:09: 210000000
INFO @ Thu, 13 Apr 2017 22:24:10: 211000000
INFO @ Thu, 13 Apr 2017 22:24:12: 212000000
INFO @ Thu, 13 Apr 2017 22:24:14: 213000000
INFO @ Thu, 13 Apr 2017 22:24:15: 214000000
INFO @ Thu, 13 Apr 2017 22:24:17: 215000000
INFO @ Thu, 13 Apr 2017 22:24:19: 216000000
INFO @ Thu, 13 Apr 2017 22:24:20: 217000000
INFO @ Thu, 13 Apr 2017 22:24:22: 218000000
INFO @ Thu, 13 Apr 2017 22:24:24: 219000000
INFO @ Thu, 13 Apr 2017 22:24:42: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:24:44: 1000000
INFO @ Thu, 13 Apr 2017 22:24:46: 2000000
INFO @ Thu, 13 Apr 2017 22:24:48: 3000000
INFO @ Thu, 13 Apr 2017 22:24:50: 4000000
INFO @ Thu, 13 Apr 2017 22:24:51: 5000000
INFO @ Thu, 13 Apr 2017 22:24:53: 6000000
INFO @ Thu, 13 Apr 2017 22:24:55: 7000000
INFO @ Thu, 13 Apr 2017 22:24:56: 8000000
INFO @ Thu, 13 Apr 2017 22:24:58: 9000000
INFO @ Thu, 13 Apr 2017 22:25:00: 10000000
INFO @ Thu, 13 Apr 2017 22:25:01: 11000000
INFO @ Thu, 13 Apr 2017 22:25:03: 12000000
INFO @ Thu, 13 Apr 2017 22:25:05: 13000000
INFO @ Thu, 13 Apr 2017 22:25:07: 14000000
INFO @ Thu, 13 Apr 2017 22:25:09: 15000000
INFO @ Thu, 13 Apr 2017 22:25:11: 16000000
INFO @ Thu, 13 Apr 2017 22:25:13: 17000000
INFO @ Thu, 13 Apr 2017 22:25:15: 18000000
INFO @ Thu, 13 Apr 2017 22:25:16: 19000000
INFO @ Thu, 13 Apr 2017 22:25:18: 20000000
INFO @ Thu, 13 Apr 2017 22:25:20: 21000000
INFO @ Thu, 13 Apr 2017 22:25:22: 22000000
INFO @ Thu, 13 Apr 2017 22:25:24: 23000000
INFO @ Thu, 13 Apr 2017 22:25:25: 24000000
INFO @ Thu, 13 Apr 2017 22:25:27: 25000000
INFO @ Thu, 13 Apr 2017 22:25:29: 26000000
INFO @ Thu, 13 Apr 2017 22:25:31: 27000000
INFO @ Thu, 13 Apr 2017 22:25:33: 28000000
INFO @ Thu, 13 Apr 2017 22:25:35: 29000000
INFO @ Thu, 13 Apr 2017 22:25:37: 30000000
INFO @ Thu, 13 Apr 2017 22:25:39: 31000000
INFO @ Thu, 13 Apr 2017 22:25:41: 32000000
INFO @ Thu, 13 Apr 2017 22:25:43: 33000000
INFO @ Thu, 13 Apr 2017 22:25:45: 34000000
INFO @ Thu, 13 Apr 2017 22:25:47: 35000000
INFO @ Thu, 13 Apr 2017 22:25:49: 36000000
INFO @ Thu, 13 Apr 2017 22:25:51: 37000000
INFO @ Thu, 13 Apr 2017 22:25:53: 38000000
INFO @ Thu, 13 Apr 2017 22:25:55: 39000000
INFO @ Thu, 13 Apr 2017 22:25:57: 40000000
INFO @ Thu, 13 Apr 2017 22:25:59: 41000000
INFO @ Thu, 13 Apr 2017 22:26:01: 42000000
INFO @ Thu, 13 Apr 2017 22:26:03: 43000000
INFO @ Thu, 13 Apr 2017 22:26:05: 44000000
INFO @ Thu, 13 Apr 2017 22:26:07: 45000000
INFO @ Thu, 13 Apr 2017 22:26:09: 46000000
INFO @ Thu, 13 Apr 2017 22:26:11: 47000000
INFO @ Thu, 13 Apr 2017 22:26:13: 48000000
INFO @ Thu, 13 Apr 2017 22:26:15: 49000000
INFO @ Thu, 13 Apr 2017 22:26:16: 50000000
INFO @ Thu, 13 Apr 2017 22:26:18: 51000000
INFO @ Thu, 13 Apr 2017 22:26:20: 52000000
INFO @ Thu, 13 Apr 2017 22:26:22: 53000000
INFO @ Thu, 13 Apr 2017 22:26:24: 54000000
INFO @ Thu, 13 Apr 2017 22:26:25: 55000000
INFO @ Thu, 13 Apr 2017 22:26:27: 56000000
INFO @ Thu, 13 Apr 2017 22:26:29: 57000000
INFO @ Thu, 13 Apr 2017 22:26:30: 58000000
INFO @ Thu, 13 Apr 2017 22:26:32: 59000000
INFO @ Thu, 13 Apr 2017 22:26:34: 60000000
INFO @ Thu, 13 Apr 2017 22:26:35: 61000000
INFO @ Thu, 13 Apr 2017 22:26:37: 62000000
INFO @ Thu, 13 Apr 2017 22:26:39: 63000000
INFO @ Thu, 13 Apr 2017 22:26:40: 64000000
INFO @ Thu, 13 Apr 2017 22:26:42: 65000000
INFO @ Thu, 13 Apr 2017 22:26:44: 66000000
INFO @ Thu, 13 Apr 2017 22:26:45: 67000000
INFO @ Thu, 13 Apr 2017 22:26:47: 68000000
INFO @ Thu, 13 Apr 2017 22:26:48: 69000000
INFO @ Thu, 13 Apr 2017 22:26:50: 70000000
INFO @ Thu, 13 Apr 2017 22:26:52: 71000000
INFO @ Thu, 13 Apr 2017 22:26:54: 72000000
INFO @ Thu, 13 Apr 2017 22:26:55: 73000000
INFO @ Thu, 13 Apr 2017 22:26:57: 74000000
INFO @ Thu, 13 Apr 2017 22:26:59: 75000000
INFO @ Thu, 13 Apr 2017 22:27:00: 76000000
INFO @ Thu, 13 Apr 2017 22:27:02: 77000000
INFO @ Thu, 13 Apr 2017 22:27:04: 78000000
INFO @ Thu, 13 Apr 2017 22:27:06: 79000000
INFO @ Thu, 13 Apr 2017 22:27:07: 80000000
INFO @ Thu, 13 Apr 2017 22:27:09: 81000000
INFO @ Thu, 13 Apr 2017 22:27:11: 82000000
INFO @ Thu, 13 Apr 2017 22:27:13: 83000000
INFO @ Thu, 13 Apr 2017 22:27:14: 84000000
INFO @ Thu, 13 Apr 2017 22:27:16: 85000000
INFO @ Thu, 13 Apr 2017 22:27:18: 86000000
INFO @ Thu, 13 Apr 2017 22:27:19: 87000000
INFO @ Thu, 13 Apr 2017 22:27:21: 88000000
INFO @ Thu, 13 Apr 2017 22:27:23: 89000000
INFO @ Thu, 13 Apr 2017 22:27:24: 90000000
INFO @ Thu, 13 Apr 2017 22:27:26: 91000000
INFO @ Thu, 13 Apr 2017 22:27:27: 92000000
INFO @ Thu, 13 Apr 2017 22:27:29: 93000000
INFO @ Thu, 13 Apr 2017 22:27:31: 94000000
INFO @ Thu, 13 Apr 2017 22:27:33: 95000000
INFO @ Thu, 13 Apr 2017 22:27:34: 96000000
INFO @ Thu, 13 Apr 2017 22:27:36: 97000000
INFO @ Thu, 13 Apr 2017 22:27:38: 98000000
INFO @ Thu, 13 Apr 2017 22:27:39: 99000000
INFO @ Thu, 13 Apr 2017 22:27:48: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:27:48: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:27:48: #1 total tags in treatment: 219735318
INFO @ Thu, 13 Apr 2017 22:27:48: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:27:48: #1 finished!
INFO @ Thu, 13 Apr 2017 22:27:48: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:27:48: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:27:48: #2 Use 238 as fragment length
INFO @ Thu, 13 Apr 2017 22:27:48: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:27:48: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:27:48: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 22:38:45: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 22:38:45: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 22:38:45: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 22:38:45: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 22:38:45: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 23:00:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 23:01:00: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 23:01:00: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 23:01:00: Done!
INFO @ Thu, 13 Apr 2017 23:01:03: Read and build treatment bedGraph...
INFO @ Thu, 13 Apr 2017 23:08:35: Read and build control bedGraph...
INFO @ Thu, 13 Apr 2017 23:11:49: Build scoreTrackII...
INFO @ Thu, 13 Apr 2017 23:15:17: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 13 Apr 2017 23:39:51: Write bedGraph of scores...
INFO @ Thu, 13 Apr 2017 23:57:58: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_FE.bdg'!
INFO @ Fri, 14 Apr 2017 00:38:12: Read and build treatment bedGraph...
INFO @ Fri, 14 Apr 2017 00:45:54: Read and build control bedGraph...
INFO @ Fri, 14 Apr 2017 00:49:23: Build scoreTrackII...
INFO @ Fri, 14 Apr 2017 00:53:43: Values in your input bedGraph files will be multiplied by 99.976272 ...
INFO @ Fri, 14 Apr 2017 01:17:21: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Fri, 14 Apr 2017 01:23:41: Write bedGraph of scores...
INFO @ Fri, 14 Apr 2017 01:33:47: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_ppois.bdg'!
|
Num | 4 | ID | task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_13 | Name | macs2 n/s ppr1 | Thread | thread_Root | PID | 47040 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:18:03 | End | 2017-04-13 22:50:38 | Elapsed | 00:32:35 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
26842 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:18:17:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:18:17: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:18:17: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:18:19: 1000000
INFO @ Thu, 13 Apr 2017 22:18:21: 2000000
INFO @ Thu, 13 Apr 2017 22:18:23: 3000000
INFO @ Thu, 13 Apr 2017 22:18:25: 4000000
INFO @ Thu, 13 Apr 2017 22:18:27: 5000000
INFO @ Thu, 13 Apr 2017 22:18:29: 6000000
INFO @ Thu, 13 Apr 2017 22:18:31: 7000000
INFO @ Thu, 13 Apr 2017 22:18:33: 8000000
INFO @ Thu, 13 Apr 2017 22:18:34: 9000000
INFO @ Thu, 13 Apr 2017 22:18:36: 10000000
INFO @ Thu, 13 Apr 2017 22:18:38: 11000000
INFO @ Thu, 13 Apr 2017 22:18:40: 12000000
INFO @ Thu, 13 Apr 2017 22:18:41: 13000000
INFO @ Thu, 13 Apr 2017 22:18:43: 14000000
INFO @ Thu, 13 Apr 2017 22:18:45: 15000000
INFO @ Thu, 13 Apr 2017 22:18:47: 16000000
INFO @ Thu, 13 Apr 2017 22:18:48: 17000000
INFO @ Thu, 13 Apr 2017 22:18:50: 18000000
INFO @ Thu, 13 Apr 2017 22:18:52: 19000000
INFO @ Thu, 13 Apr 2017 22:18:54: 20000000
INFO @ Thu, 13 Apr 2017 22:18:55: 21000000
INFO @ Thu, 13 Apr 2017 22:18:57: 22000000
INFO @ Thu, 13 Apr 2017 22:18:59: 23000000
INFO @ Thu, 13 Apr 2017 22:19:01: 24000000
INFO @ Thu, 13 Apr 2017 22:19:02: 25000000
INFO @ Thu, 13 Apr 2017 22:19:04: 26000000
INFO @ Thu, 13 Apr 2017 22:19:06: 27000000
INFO @ Thu, 13 Apr 2017 22:19:08: 28000000
INFO @ Thu, 13 Apr 2017 22:19:09: 29000000
INFO @ Thu, 13 Apr 2017 22:19:11: 30000000
INFO @ Thu, 13 Apr 2017 22:19:13: 31000000
INFO @ Thu, 13 Apr 2017 22:19:15: 32000000
INFO @ Thu, 13 Apr 2017 22:19:16: 33000000
INFO @ Thu, 13 Apr 2017 22:19:18: 34000000
INFO @ Thu, 13 Apr 2017 22:19:20: 35000000
INFO @ Thu, 13 Apr 2017 22:19:22: 36000000
INFO @ Thu, 13 Apr 2017 22:19:23: 37000000
INFO @ Thu, 13 Apr 2017 22:19:25: 38000000
INFO @ Thu, 13 Apr 2017 22:19:27: 39000000
INFO @ Thu, 13 Apr 2017 22:19:29: 40000000
INFO @ Thu, 13 Apr 2017 22:19:30: 41000000
INFO @ Thu, 13 Apr 2017 22:19:32: 42000000
INFO @ Thu, 13 Apr 2017 22:19:34: 43000000
INFO @ Thu, 13 Apr 2017 22:19:36: 44000000
INFO @ Thu, 13 Apr 2017 22:19:37: 45000000
INFO @ Thu, 13 Apr 2017 22:19:39: 46000000
INFO @ Thu, 13 Apr 2017 22:19:41: 47000000
INFO @ Thu, 13 Apr 2017 22:19:42: 48000000
INFO @ Thu, 13 Apr 2017 22:19:44: 49000000
INFO @ Thu, 13 Apr 2017 22:19:46: 50000000
INFO @ Thu, 13 Apr 2017 22:19:48: 51000000
INFO @ Thu, 13 Apr 2017 22:19:49: 52000000
INFO @ Thu, 13 Apr 2017 22:19:51: 53000000
INFO @ Thu, 13 Apr 2017 22:19:53: 54000000
INFO @ Thu, 13 Apr 2017 22:19:55: 55000000
INFO @ Thu, 13 Apr 2017 22:19:56: 56000000
INFO @ Thu, 13 Apr 2017 22:19:58: 57000000
INFO @ Thu, 13 Apr 2017 22:20:00: 58000000
INFO @ Thu, 13 Apr 2017 22:20:01: 59000000
INFO @ Thu, 13 Apr 2017 22:20:03: 60000000
INFO @ Thu, 13 Apr 2017 22:20:05: 61000000
INFO @ Thu, 13 Apr 2017 22:20:07: 62000000
INFO @ Thu, 13 Apr 2017 22:20:08: 63000000
INFO @ Thu, 13 Apr 2017 22:20:10: 64000000
INFO @ Thu, 13 Apr 2017 22:20:12: 65000000
INFO @ Thu, 13 Apr 2017 22:20:14: 66000000
INFO @ Thu, 13 Apr 2017 22:20:15: 67000000
INFO @ Thu, 13 Apr 2017 22:20:17: 68000000
INFO @ Thu, 13 Apr 2017 22:20:19: 69000000
INFO @ Thu, 13 Apr 2017 22:20:21: 70000000
INFO @ Thu, 13 Apr 2017 22:20:22: 71000000
INFO @ Thu, 13 Apr 2017 22:20:24: 72000000
INFO @ Thu, 13 Apr 2017 22:20:26: 73000000
INFO @ Thu, 13 Apr 2017 22:20:28: 74000000
INFO @ Thu, 13 Apr 2017 22:20:29: 75000000
INFO @ Thu, 13 Apr 2017 22:20:31: 76000000
INFO @ Thu, 13 Apr 2017 22:20:33: 77000000
INFO @ Thu, 13 Apr 2017 22:20:34: 78000000
INFO @ Thu, 13 Apr 2017 22:20:36: 79000000
INFO @ Thu, 13 Apr 2017 22:20:38: 80000000
INFO @ Thu, 13 Apr 2017 22:20:40: 81000000
INFO @ Thu, 13 Apr 2017 22:20:41: 82000000
INFO @ Thu, 13 Apr 2017 22:20:43: 83000000
INFO @ Thu, 13 Apr 2017 22:20:45: 84000000
INFO @ Thu, 13 Apr 2017 22:20:47: 85000000
INFO @ Thu, 13 Apr 2017 22:20:48: 86000000
INFO @ Thu, 13 Apr 2017 22:20:50: 87000000
INFO @ Thu, 13 Apr 2017 22:20:52: 88000000
INFO @ Thu, 13 Apr 2017 22:20:54: 89000000
INFO @ Thu, 13 Apr 2017 22:20:55: 90000000
INFO @ Thu, 13 Apr 2017 22:20:57: 91000000
INFO @ Thu, 13 Apr 2017 22:20:59: 92000000
INFO @ Thu, 13 Apr 2017 22:21:01: 93000000
INFO @ Thu, 13 Apr 2017 22:21:02: 94000000
INFO @ Thu, 13 Apr 2017 22:21:04: 95000000
INFO @ Thu, 13 Apr 2017 22:21:06: 96000000
INFO @ Thu, 13 Apr 2017 22:21:08: 97000000
INFO @ Thu, 13 Apr 2017 22:21:09: 98000000
INFO @ Thu, 13 Apr 2017 22:21:11: 99000000
INFO @ Thu, 13 Apr 2017 22:21:13: 100000000
INFO @ Thu, 13 Apr 2017 22:21:14: 101000000
INFO @ Thu, 13 Apr 2017 22:21:16: 102000000
INFO @ Thu, 13 Apr 2017 22:21:18: 103000000
INFO @ Thu, 13 Apr 2017 22:21:20: 104000000
INFO @ Thu, 13 Apr 2017 22:21:21: 105000000
INFO @ Thu, 13 Apr 2017 22:21:23: 106000000
INFO @ Thu, 13 Apr 2017 22:21:25: 107000000
INFO @ Thu, 13 Apr 2017 22:21:27: 108000000
INFO @ Thu, 13 Apr 2017 22:21:28: 109000000
INFO @ Thu, 13 Apr 2017 22:21:38: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:21:40: 1000000
INFO @ Thu, 13 Apr 2017 22:21:42: 2000000
INFO @ Thu, 13 Apr 2017 22:21:44: 3000000
INFO @ Thu, 13 Apr 2017 22:21:45: 4000000
INFO @ Thu, 13 Apr 2017 22:21:47: 5000000
INFO @ Thu, 13 Apr 2017 22:21:49: 6000000
INFO @ Thu, 13 Apr 2017 22:21:51: 7000000
INFO @ Thu, 13 Apr 2017 22:21:52: 8000000
INFO @ Thu, 13 Apr 2017 22:21:54: 9000000
INFO @ Thu, 13 Apr 2017 22:21:56: 10000000
INFO @ Thu, 13 Apr 2017 22:21:58: 11000000
INFO @ Thu, 13 Apr 2017 22:21:59: 12000000
INFO @ Thu, 13 Apr 2017 22:22:01: 13000000
INFO @ Thu, 13 Apr 2017 22:22:03: 14000000
INFO @ Thu, 13 Apr 2017 22:22:04: 15000000
INFO @ Thu, 13 Apr 2017 22:22:06: 16000000
INFO @ Thu, 13 Apr 2017 22:22:08: 17000000
INFO @ Thu, 13 Apr 2017 22:22:10: 18000000
INFO @ Thu, 13 Apr 2017 22:22:11: 19000000
INFO @ Thu, 13 Apr 2017 22:22:13: 20000000
INFO @ Thu, 13 Apr 2017 22:22:15: 21000000
INFO @ Thu, 13 Apr 2017 22:22:17: 22000000
INFO @ Thu, 13 Apr 2017 22:22:18: 23000000
INFO @ Thu, 13 Apr 2017 22:22:20: 24000000
INFO @ Thu, 13 Apr 2017 22:22:22: 25000000
INFO @ Thu, 13 Apr 2017 22:22:24: 26000000
INFO @ Thu, 13 Apr 2017 22:22:25: 27000000
INFO @ Thu, 13 Apr 2017 22:22:27: 28000000
INFO @ Thu, 13 Apr 2017 22:22:29: 29000000
INFO @ Thu, 13 Apr 2017 22:22:31: 30000000
INFO @ Thu, 13 Apr 2017 22:22:32: 31000000
INFO @ Thu, 13 Apr 2017 22:22:34: 32000000
INFO @ Thu, 13 Apr 2017 22:22:36: 33000000
INFO @ Thu, 13 Apr 2017 22:22:38: 34000000
INFO @ Thu, 13 Apr 2017 22:22:39: 35000000
INFO @ Thu, 13 Apr 2017 22:22:41: 36000000
INFO @ Thu, 13 Apr 2017 22:22:43: 37000000
INFO @ Thu, 13 Apr 2017 22:22:45: 38000000
INFO @ Thu, 13 Apr 2017 22:22:46: 39000000
INFO @ Thu, 13 Apr 2017 22:22:48: 40000000
INFO @ Thu, 13 Apr 2017 22:22:50: 41000000
INFO @ Thu, 13 Apr 2017 22:22:52: 42000000
INFO @ Thu, 13 Apr 2017 22:22:53: 43000000
INFO @ Thu, 13 Apr 2017 22:22:55: 44000000
INFO @ Thu, 13 Apr 2017 22:22:57: 45000000
INFO @ Thu, 13 Apr 2017 22:22:58: 46000000
INFO @ Thu, 13 Apr 2017 22:23:00: 47000000
INFO @ Thu, 13 Apr 2017 22:23:02: 48000000
INFO @ Thu, 13 Apr 2017 22:23:04: 49000000
INFO @ Thu, 13 Apr 2017 22:23:06: 50000000
INFO @ Thu, 13 Apr 2017 22:23:07: 51000000
INFO @ Thu, 13 Apr 2017 22:23:09: 52000000
INFO @ Thu, 13 Apr 2017 22:23:11: 53000000
INFO @ Thu, 13 Apr 2017 22:23:12: 54000000
INFO @ Thu, 13 Apr 2017 22:23:14: 55000000
INFO @ Thu, 13 Apr 2017 22:23:16: 56000000
INFO @ Thu, 13 Apr 2017 22:23:18: 57000000
INFO @ Thu, 13 Apr 2017 22:23:20: 58000000
INFO @ Thu, 13 Apr 2017 22:23:21: 59000000
INFO @ Thu, 13 Apr 2017 22:23:23: 60000000
INFO @ Thu, 13 Apr 2017 22:23:25: 61000000
INFO @ Thu, 13 Apr 2017 22:23:26: 62000000
INFO @ Thu, 13 Apr 2017 22:23:28: 63000000
INFO @ Thu, 13 Apr 2017 22:23:30: 64000000
INFO @ Thu, 13 Apr 2017 22:23:32: 65000000
INFO @ Thu, 13 Apr 2017 22:23:33: 66000000
INFO @ Thu, 13 Apr 2017 22:23:35: 67000000
INFO @ Thu, 13 Apr 2017 22:23:37: 68000000
INFO @ Thu, 13 Apr 2017 22:23:39: 69000000
INFO @ Thu, 13 Apr 2017 22:23:40: 70000000
INFO @ Thu, 13 Apr 2017 22:23:42: 71000000
INFO @ Thu, 13 Apr 2017 22:23:44: 72000000
INFO @ Thu, 13 Apr 2017 22:23:45: 73000000
INFO @ Thu, 13 Apr 2017 22:23:47: 74000000
INFO @ Thu, 13 Apr 2017 22:23:49: 75000000
INFO @ Thu, 13 Apr 2017 22:23:51: 76000000
INFO @ Thu, 13 Apr 2017 22:23:52: 77000000
INFO @ Thu, 13 Apr 2017 22:23:54: 78000000
INFO @ Thu, 13 Apr 2017 22:23:56: 79000000
INFO @ Thu, 13 Apr 2017 22:23:58: 80000000
INFO @ Thu, 13 Apr 2017 22:23:59: 81000000
INFO @ Thu, 13 Apr 2017 22:24:01: 82000000
INFO @ Thu, 13 Apr 2017 22:24:03: 83000000
INFO @ Thu, 13 Apr 2017 22:24:05: 84000000
INFO @ Thu, 13 Apr 2017 22:24:06: 85000000
INFO @ Thu, 13 Apr 2017 22:24:08: 86000000
INFO @ Thu, 13 Apr 2017 22:24:10: 87000000
INFO @ Thu, 13 Apr 2017 22:24:12: 88000000
INFO @ Thu, 13 Apr 2017 22:24:14: 89000000
INFO @ Thu, 13 Apr 2017 22:24:15: 90000000
INFO @ Thu, 13 Apr 2017 22:24:17: 91000000
INFO @ Thu, 13 Apr 2017 22:24:19: 92000000
INFO @ Thu, 13 Apr 2017 22:24:21: 93000000
INFO @ Thu, 13 Apr 2017 22:24:22: 94000000
INFO @ Thu, 13 Apr 2017 22:24:24: 95000000
INFO @ Thu, 13 Apr 2017 22:24:26: 96000000
INFO @ Thu, 13 Apr 2017 22:24:28: 97000000
INFO @ Thu, 13 Apr 2017 22:24:29: 98000000
INFO @ Thu, 13 Apr 2017 22:24:31: 99000000
INFO @ Thu, 13 Apr 2017 22:24:40: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:24:40: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:24:40: #1 total tags in treatment: 109867660
INFO @ Thu, 13 Apr 2017 22:24:40: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:24:40: #1 finished!
INFO @ Thu, 13 Apr 2017 22:24:40: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:24:40: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:24:40: #2 Use 238 as fragment length
INFO @ Thu, 13 Apr 2017 22:24:40: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:24:40: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:24:40: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 22:33:48: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 22:33:48: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 22:33:48: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 22:33:48: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 22:33:48: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 22:50:33: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 22:50:33: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 22:50:34: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 22:50:34: Done!
|
Num | 5 | ID | task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_14 | Name | macs2 n/s ppr2 | Thread | thread_Root | PID | 47041 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:18:05 | End | 2017-04-13 22:52:03 | Elapsed | 00:33:58 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
26840 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:18:17:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:18:17: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:18:17: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:18:19: 1000000
INFO @ Thu, 13 Apr 2017 22:18:21: 2000000
INFO @ Thu, 13 Apr 2017 22:18:23: 3000000
INFO @ Thu, 13 Apr 2017 22:18:25: 4000000
INFO @ Thu, 13 Apr 2017 22:18:27: 5000000
INFO @ Thu, 13 Apr 2017 22:18:30: 6000000
INFO @ Thu, 13 Apr 2017 22:18:32: 7000000
INFO @ Thu, 13 Apr 2017 22:18:34: 8000000
INFO @ Thu, 13 Apr 2017 22:18:36: 9000000
INFO @ Thu, 13 Apr 2017 22:18:38: 10000000
INFO @ Thu, 13 Apr 2017 22:18:40: 11000000
INFO @ Thu, 13 Apr 2017 22:18:42: 12000000
INFO @ Thu, 13 Apr 2017 22:18:44: 13000000
INFO @ Thu, 13 Apr 2017 22:18:47: 14000000
INFO @ Thu, 13 Apr 2017 22:18:49: 15000000
INFO @ Thu, 13 Apr 2017 22:18:51: 16000000
INFO @ Thu, 13 Apr 2017 22:18:53: 17000000
INFO @ Thu, 13 Apr 2017 22:18:55: 18000000
INFO @ Thu, 13 Apr 2017 22:18:57: 19000000
INFO @ Thu, 13 Apr 2017 22:18:59: 20000000
INFO @ Thu, 13 Apr 2017 22:19:01: 21000000
INFO @ Thu, 13 Apr 2017 22:19:03: 22000000
INFO @ Thu, 13 Apr 2017 22:19:05: 23000000
INFO @ Thu, 13 Apr 2017 22:19:07: 24000000
INFO @ Thu, 13 Apr 2017 22:19:10: 25000000
INFO @ Thu, 13 Apr 2017 22:19:12: 26000000
INFO @ Thu, 13 Apr 2017 22:19:14: 27000000
INFO @ Thu, 13 Apr 2017 22:19:16: 28000000
INFO @ Thu, 13 Apr 2017 22:19:18: 29000000
INFO @ Thu, 13 Apr 2017 22:19:20: 30000000
INFO @ Thu, 13 Apr 2017 22:19:22: 31000000
INFO @ Thu, 13 Apr 2017 22:19:24: 32000000
INFO @ Thu, 13 Apr 2017 22:19:26: 33000000
INFO @ Thu, 13 Apr 2017 22:19:28: 34000000
INFO @ Thu, 13 Apr 2017 22:19:30: 35000000
INFO @ Thu, 13 Apr 2017 22:19:32: 36000000
INFO @ Thu, 13 Apr 2017 22:19:34: 37000000
INFO @ Thu, 13 Apr 2017 22:19:37: 38000000
INFO @ Thu, 13 Apr 2017 22:19:39: 39000000
INFO @ Thu, 13 Apr 2017 22:19:41: 40000000
INFO @ Thu, 13 Apr 2017 22:19:43: 41000000
INFO @ Thu, 13 Apr 2017 22:19:45: 42000000
INFO @ Thu, 13 Apr 2017 22:19:47: 43000000
INFO @ Thu, 13 Apr 2017 22:19:49: 44000000
INFO @ Thu, 13 Apr 2017 22:19:51: 45000000
INFO @ Thu, 13 Apr 2017 22:19:53: 46000000
INFO @ Thu, 13 Apr 2017 22:19:55: 47000000
INFO @ Thu, 13 Apr 2017 22:19:58: 48000000
INFO @ Thu, 13 Apr 2017 22:20:00: 49000000
INFO @ Thu, 13 Apr 2017 22:20:02: 50000000
INFO @ Thu, 13 Apr 2017 22:20:04: 51000000
INFO @ Thu, 13 Apr 2017 22:20:06: 52000000
INFO @ Thu, 13 Apr 2017 22:20:08: 53000000
INFO @ Thu, 13 Apr 2017 22:20:10: 54000000
INFO @ Thu, 13 Apr 2017 22:20:12: 55000000
INFO @ Thu, 13 Apr 2017 22:20:14: 56000000
INFO @ Thu, 13 Apr 2017 22:20:16: 57000000
INFO @ Thu, 13 Apr 2017 22:20:19: 58000000
INFO @ Thu, 13 Apr 2017 22:20:21: 59000000
INFO @ Thu, 13 Apr 2017 22:20:23: 60000000
INFO @ Thu, 13 Apr 2017 22:20:25: 61000000
INFO @ Thu, 13 Apr 2017 22:20:27: 62000000
INFO @ Thu, 13 Apr 2017 22:20:29: 63000000
INFO @ Thu, 13 Apr 2017 22:20:31: 64000000
INFO @ Thu, 13 Apr 2017 22:20:33: 65000000
INFO @ Thu, 13 Apr 2017 22:20:36: 66000000
INFO @ Thu, 13 Apr 2017 22:20:38: 67000000
INFO @ Thu, 13 Apr 2017 22:20:40: 68000000
INFO @ Thu, 13 Apr 2017 22:20:42: 69000000
INFO @ Thu, 13 Apr 2017 22:20:44: 70000000
INFO @ Thu, 13 Apr 2017 22:20:46: 71000000
INFO @ Thu, 13 Apr 2017 22:20:48: 72000000
INFO @ Thu, 13 Apr 2017 22:20:50: 73000000
INFO @ Thu, 13 Apr 2017 22:20:52: 74000000
INFO @ Thu, 13 Apr 2017 22:20:54: 75000000
INFO @ Thu, 13 Apr 2017 22:20:56: 76000000
INFO @ Thu, 13 Apr 2017 22:20:58: 77000000
INFO @ Thu, 13 Apr 2017 22:21:00: 78000000
INFO @ Thu, 13 Apr 2017 22:21:03: 79000000
INFO @ Thu, 13 Apr 2017 22:21:05: 80000000
INFO @ Thu, 13 Apr 2017 22:21:07: 81000000
INFO @ Thu, 13 Apr 2017 22:21:09: 82000000
INFO @ Thu, 13 Apr 2017 22:21:11: 83000000
INFO @ Thu, 13 Apr 2017 22:21:13: 84000000
INFO @ Thu, 13 Apr 2017 22:21:15: 85000000
INFO @ Thu, 13 Apr 2017 22:21:17: 86000000
INFO @ Thu, 13 Apr 2017 22:21:19: 87000000
INFO @ Thu, 13 Apr 2017 22:21:21: 88000000
INFO @ Thu, 13 Apr 2017 22:21:23: 89000000
INFO @ Thu, 13 Apr 2017 22:21:26: 90000000
INFO @ Thu, 13 Apr 2017 22:21:28: 91000000
INFO @ Thu, 13 Apr 2017 22:21:30: 92000000
INFO @ Thu, 13 Apr 2017 22:21:32: 93000000
INFO @ Thu, 13 Apr 2017 22:21:34: 94000000
INFO @ Thu, 13 Apr 2017 22:21:36: 95000000
INFO @ Thu, 13 Apr 2017 22:21:38: 96000000
INFO @ Thu, 13 Apr 2017 22:21:40: 97000000
INFO @ Thu, 13 Apr 2017 22:21:42: 98000000
INFO @ Thu, 13 Apr 2017 22:21:44: 99000000
INFO @ Thu, 13 Apr 2017 22:21:47: 100000000
INFO @ Thu, 13 Apr 2017 22:21:49: 101000000
INFO @ Thu, 13 Apr 2017 22:21:51: 102000000
INFO @ Thu, 13 Apr 2017 22:21:53: 103000000
INFO @ Thu, 13 Apr 2017 22:21:55: 104000000
INFO @ Thu, 13 Apr 2017 22:21:57: 105000000
INFO @ Thu, 13 Apr 2017 22:21:59: 106000000
INFO @ Thu, 13 Apr 2017 22:22:01: 107000000
INFO @ Thu, 13 Apr 2017 22:22:03: 108000000
INFO @ Thu, 13 Apr 2017 22:22:05: 109000000
INFO @ Thu, 13 Apr 2017 22:22:17: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:22:19: 1000000
INFO @ Thu, 13 Apr 2017 22:22:21: 2000000
INFO @ Thu, 13 Apr 2017 22:22:23: 3000000
INFO @ Thu, 13 Apr 2017 22:22:25: 4000000
INFO @ Thu, 13 Apr 2017 22:22:28: 5000000
INFO @ Thu, 13 Apr 2017 22:22:30: 6000000
INFO @ Thu, 13 Apr 2017 22:22:32: 7000000
INFO @ Thu, 13 Apr 2017 22:22:34: 8000000
INFO @ Thu, 13 Apr 2017 22:22:36: 9000000
INFO @ Thu, 13 Apr 2017 22:22:38: 10000000
INFO @ Thu, 13 Apr 2017 22:22:40: 11000000
INFO @ Thu, 13 Apr 2017 22:22:42: 12000000
INFO @ Thu, 13 Apr 2017 22:22:44: 13000000
INFO @ Thu, 13 Apr 2017 22:22:47: 14000000
INFO @ Thu, 13 Apr 2017 22:22:49: 15000000
INFO @ Thu, 13 Apr 2017 22:22:51: 16000000
INFO @ Thu, 13 Apr 2017 22:22:53: 17000000
INFO @ Thu, 13 Apr 2017 22:22:55: 18000000
INFO @ Thu, 13 Apr 2017 22:22:57: 19000000
INFO @ Thu, 13 Apr 2017 22:22:59: 20000000
INFO @ Thu, 13 Apr 2017 22:23:01: 21000000
INFO @ Thu, 13 Apr 2017 22:23:03: 22000000
INFO @ Thu, 13 Apr 2017 22:23:05: 23000000
INFO @ Thu, 13 Apr 2017 22:23:07: 24000000
INFO @ Thu, 13 Apr 2017 22:23:10: 25000000
INFO @ Thu, 13 Apr 2017 22:23:12: 26000000
INFO @ Thu, 13 Apr 2017 22:23:14: 27000000
INFO @ Thu, 13 Apr 2017 22:23:16: 28000000
INFO @ Thu, 13 Apr 2017 22:23:18: 29000000
INFO @ Thu, 13 Apr 2017 22:23:20: 30000000
INFO @ Thu, 13 Apr 2017 22:23:22: 31000000
INFO @ Thu, 13 Apr 2017 22:23:25: 32000000
INFO @ Thu, 13 Apr 2017 22:23:27: 33000000
INFO @ Thu, 13 Apr 2017 22:23:29: 34000000
INFO @ Thu, 13 Apr 2017 22:23:31: 35000000
INFO @ Thu, 13 Apr 2017 22:23:33: 36000000
INFO @ Thu, 13 Apr 2017 22:23:35: 37000000
INFO @ Thu, 13 Apr 2017 22:23:38: 38000000
INFO @ Thu, 13 Apr 2017 22:23:40: 39000000
INFO @ Thu, 13 Apr 2017 22:23:42: 40000000
INFO @ Thu, 13 Apr 2017 22:23:44: 41000000
INFO @ Thu, 13 Apr 2017 22:23:46: 42000000
INFO @ Thu, 13 Apr 2017 22:23:48: 43000000
INFO @ Thu, 13 Apr 2017 22:23:50: 44000000
INFO @ Thu, 13 Apr 2017 22:23:52: 45000000
INFO @ Thu, 13 Apr 2017 22:23:54: 46000000
INFO @ Thu, 13 Apr 2017 22:23:57: 47000000
INFO @ Thu, 13 Apr 2017 22:23:59: 48000000
INFO @ Thu, 13 Apr 2017 22:24:01: 49000000
INFO @ Thu, 13 Apr 2017 22:24:03: 50000000
INFO @ Thu, 13 Apr 2017 22:24:05: 51000000
INFO @ Thu, 13 Apr 2017 22:24:07: 52000000
INFO @ Thu, 13 Apr 2017 22:24:09: 53000000
INFO @ Thu, 13 Apr 2017 22:24:11: 54000000
INFO @ Thu, 13 Apr 2017 22:24:13: 55000000
INFO @ Thu, 13 Apr 2017 22:24:15: 56000000
INFO @ Thu, 13 Apr 2017 22:24:17: 57000000
INFO @ Thu, 13 Apr 2017 22:24:20: 58000000
INFO @ Thu, 13 Apr 2017 22:24:22: 59000000
INFO @ Thu, 13 Apr 2017 22:24:24: 60000000
INFO @ Thu, 13 Apr 2017 22:24:26: 61000000
INFO @ Thu, 13 Apr 2017 22:24:28: 62000000
INFO @ Thu, 13 Apr 2017 22:24:30: 63000000
INFO @ Thu, 13 Apr 2017 22:24:32: 64000000
INFO @ Thu, 13 Apr 2017 22:24:34: 65000000
INFO @ Thu, 13 Apr 2017 22:24:36: 66000000
INFO @ Thu, 13 Apr 2017 22:24:38: 67000000
INFO @ Thu, 13 Apr 2017 22:24:40: 68000000
INFO @ Thu, 13 Apr 2017 22:24:42: 69000000
INFO @ Thu, 13 Apr 2017 22:24:45: 70000000
INFO @ Thu, 13 Apr 2017 22:24:47: 71000000
INFO @ Thu, 13 Apr 2017 22:24:49: 72000000
INFO @ Thu, 13 Apr 2017 22:24:51: 73000000
INFO @ Thu, 13 Apr 2017 22:24:53: 74000000
INFO @ Thu, 13 Apr 2017 22:24:55: 75000000
INFO @ Thu, 13 Apr 2017 22:24:57: 76000000
INFO @ Thu, 13 Apr 2017 22:24:59: 77000000
INFO @ Thu, 13 Apr 2017 22:25:01: 78000000
INFO @ Thu, 13 Apr 2017 22:25:04: 79000000
INFO @ Thu, 13 Apr 2017 22:25:06: 80000000
INFO @ Thu, 13 Apr 2017 22:25:08: 81000000
INFO @ Thu, 13 Apr 2017 22:25:10: 82000000
INFO @ Thu, 13 Apr 2017 22:25:12: 83000000
INFO @ Thu, 13 Apr 2017 22:25:14: 84000000
INFO @ Thu, 13 Apr 2017 22:25:16: 85000000
INFO @ Thu, 13 Apr 2017 22:25:19: 86000000
INFO @ Thu, 13 Apr 2017 22:25:21: 87000000
INFO @ Thu, 13 Apr 2017 22:25:23: 88000000
INFO @ Thu, 13 Apr 2017 22:25:25: 89000000
INFO @ Thu, 13 Apr 2017 22:25:27: 90000000
INFO @ Thu, 13 Apr 2017 22:25:29: 91000000
INFO @ Thu, 13 Apr 2017 22:25:32: 92000000
INFO @ Thu, 13 Apr 2017 22:25:34: 93000000
INFO @ Thu, 13 Apr 2017 22:25:36: 94000000
INFO @ Thu, 13 Apr 2017 22:25:38: 95000000
INFO @ Thu, 13 Apr 2017 22:25:40: 96000000
INFO @ Thu, 13 Apr 2017 22:25:42: 97000000
INFO @ Thu, 13 Apr 2017 22:25:44: 98000000
INFO @ Thu, 13 Apr 2017 22:25:46: 99000000
INFO @ Thu, 13 Apr 2017 22:25:57: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:25:57: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:25:57: #1 total tags in treatment: 109867658
INFO @ Thu, 13 Apr 2017 22:25:57: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:25:57: #1 finished!
INFO @ Thu, 13 Apr 2017 22:25:57: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:25:57: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:25:57: #2 Use 238 as fragment length
INFO @ Thu, 13 Apr 2017 22:25:57: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:25:57: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:25:57: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 22:35:49: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 22:35:49: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 22:35:49: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 22:35:49: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 22:35:49: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 22:51:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 22:51:59: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 22:51:59: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 22:51:59: Done!
|
Num | 6 | ID | task.callpeak_macs2.macs2_n_s_rep1.line_66.id_15 | Name | macs2 n/s rep1 | Thread | thread_Root | PID | 47042 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:18:05 | End | 2017-04-14 00:22:37 | Elapsed | 02:04:31 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1 -o "ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1 -o "ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
23413 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:18:16:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:18:16: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:18:16: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:18:18: 1000000
INFO @ Thu, 13 Apr 2017 22:18:19: 2000000
INFO @ Thu, 13 Apr 2017 22:18:21: 3000000
INFO @ Thu, 13 Apr 2017 22:18:22: 4000000
INFO @ Thu, 13 Apr 2017 22:18:24: 5000000
INFO @ Thu, 13 Apr 2017 22:18:25: 6000000
INFO @ Thu, 13 Apr 2017 22:18:26: 7000000
INFO @ Thu, 13 Apr 2017 22:18:28: 8000000
INFO @ Thu, 13 Apr 2017 22:18:29: 9000000
INFO @ Thu, 13 Apr 2017 22:18:31: 10000000
INFO @ Thu, 13 Apr 2017 22:18:32: 11000000
INFO @ Thu, 13 Apr 2017 22:18:34: 12000000
INFO @ Thu, 13 Apr 2017 22:18:35: 13000000
INFO @ Thu, 13 Apr 2017 22:18:36: 14000000
INFO @ Thu, 13 Apr 2017 22:18:38: 15000000
INFO @ Thu, 13 Apr 2017 22:18:39: 16000000
INFO @ Thu, 13 Apr 2017 22:18:41: 17000000
INFO @ Thu, 13 Apr 2017 22:18:42: 18000000
INFO @ Thu, 13 Apr 2017 22:18:44: 19000000
INFO @ Thu, 13 Apr 2017 22:18:45: 20000000
INFO @ Thu, 13 Apr 2017 22:18:47: 21000000
INFO @ Thu, 13 Apr 2017 22:18:48: 22000000
INFO @ Thu, 13 Apr 2017 22:18:49: 23000000
INFO @ Thu, 13 Apr 2017 22:18:51: 24000000
INFO @ Thu, 13 Apr 2017 22:18:52: 25000000
INFO @ Thu, 13 Apr 2017 22:18:54: 26000000
INFO @ Thu, 13 Apr 2017 22:18:55: 27000000
INFO @ Thu, 13 Apr 2017 22:18:57: 28000000
INFO @ Thu, 13 Apr 2017 22:18:58: 29000000
INFO @ Thu, 13 Apr 2017 22:18:59: 30000000
INFO @ Thu, 13 Apr 2017 22:19:01: 31000000
INFO @ Thu, 13 Apr 2017 22:19:02: 32000000
INFO @ Thu, 13 Apr 2017 22:19:04: 33000000
INFO @ Thu, 13 Apr 2017 22:19:05: 34000000
INFO @ Thu, 13 Apr 2017 22:19:07: 35000000
INFO @ Thu, 13 Apr 2017 22:19:08: 36000000
INFO @ Thu, 13 Apr 2017 22:19:10: 37000000
INFO @ Thu, 13 Apr 2017 22:19:11: 38000000
INFO @ Thu, 13 Apr 2017 22:19:13: 39000000
INFO @ Thu, 13 Apr 2017 22:19:14: 40000000
INFO @ Thu, 13 Apr 2017 22:19:16: 41000000
INFO @ Thu, 13 Apr 2017 22:19:17: 42000000
INFO @ Thu, 13 Apr 2017 22:19:18: 43000000
INFO @ Thu, 13 Apr 2017 22:19:20: 44000000
INFO @ Thu, 13 Apr 2017 22:19:21: 45000000
INFO @ Thu, 13 Apr 2017 22:19:23: 46000000
INFO @ Thu, 13 Apr 2017 22:19:24: 47000000
INFO @ Thu, 13 Apr 2017 22:19:26: 48000000
INFO @ Thu, 13 Apr 2017 22:19:27: 49000000
INFO @ Thu, 13 Apr 2017 22:19:28: 50000000
INFO @ Thu, 13 Apr 2017 22:19:30: 51000000
INFO @ Thu, 13 Apr 2017 22:19:32: 52000000
INFO @ Thu, 13 Apr 2017 22:19:33: 53000000
INFO @ Thu, 13 Apr 2017 22:19:34: 54000000
INFO @ Thu, 13 Apr 2017 22:19:36: 55000000
INFO @ Thu, 13 Apr 2017 22:19:37: 56000000
INFO @ Thu, 13 Apr 2017 22:19:39: 57000000
INFO @ Thu, 13 Apr 2017 22:19:40: 58000000
INFO @ Thu, 13 Apr 2017 22:19:42: 59000000
INFO @ Thu, 13 Apr 2017 22:19:43: 60000000
INFO @ Thu, 13 Apr 2017 22:19:45: 61000000
INFO @ Thu, 13 Apr 2017 22:19:46: 62000000
INFO @ Thu, 13 Apr 2017 22:19:48: 63000000
INFO @ Thu, 13 Apr 2017 22:19:49: 64000000
INFO @ Thu, 13 Apr 2017 22:19:50: 65000000
INFO @ Thu, 13 Apr 2017 22:19:52: 66000000
INFO @ Thu, 13 Apr 2017 22:19:53: 67000000
INFO @ Thu, 13 Apr 2017 22:19:55: 68000000
INFO @ Thu, 13 Apr 2017 22:19:56: 69000000
INFO @ Thu, 13 Apr 2017 22:19:58: 70000000
INFO @ Thu, 13 Apr 2017 22:19:59: 71000000
INFO @ Thu, 13 Apr 2017 22:20:01: 72000000
INFO @ Thu, 13 Apr 2017 22:20:02: 73000000
INFO @ Thu, 13 Apr 2017 22:20:04: 74000000
INFO @ Thu, 13 Apr 2017 22:20:06: 75000000
INFO @ Thu, 13 Apr 2017 22:20:07: 76000000
INFO @ Thu, 13 Apr 2017 22:20:08: 77000000
INFO @ Thu, 13 Apr 2017 22:20:10: 78000000
INFO @ Thu, 13 Apr 2017 22:20:11: 79000000
INFO @ Thu, 13 Apr 2017 22:20:13: 80000000
INFO @ Thu, 13 Apr 2017 22:20:14: 81000000
INFO @ Thu, 13 Apr 2017 22:20:16: 82000000
INFO @ Thu, 13 Apr 2017 22:20:17: 83000000
INFO @ Thu, 13 Apr 2017 22:20:18: 84000000
INFO @ Thu, 13 Apr 2017 22:20:20: 85000000
INFO @ Thu, 13 Apr 2017 22:20:21: 86000000
INFO @ Thu, 13 Apr 2017 22:20:23: 87000000
INFO @ Thu, 13 Apr 2017 22:20:24: 88000000
INFO @ Thu, 13 Apr 2017 22:20:26: 89000000
INFO @ Thu, 13 Apr 2017 22:20:27: 90000000
INFO @ Thu, 13 Apr 2017 22:20:28: 91000000
INFO @ Thu, 13 Apr 2017 22:20:30: 92000000
INFO @ Thu, 13 Apr 2017 22:20:31: 93000000
INFO @ Thu, 13 Apr 2017 22:20:33: 94000000
INFO @ Thu, 13 Apr 2017 22:20:34: 95000000
INFO @ Thu, 13 Apr 2017 22:20:36: 96000000
INFO @ Thu, 13 Apr 2017 22:20:37: 97000000
INFO @ Thu, 13 Apr 2017 22:20:38: 98000000
INFO @ Thu, 13 Apr 2017 22:20:40: 99000000
INFO @ Thu, 13 Apr 2017 22:20:41: 100000000
INFO @ Thu, 13 Apr 2017 22:20:43: 101000000
INFO @ Thu, 13 Apr 2017 22:20:44: 102000000
INFO @ Thu, 13 Apr 2017 22:20:46: 103000000
INFO @ Thu, 13 Apr 2017 22:20:47: 104000000
INFO @ Thu, 13 Apr 2017 22:20:49: 105000000
INFO @ Thu, 13 Apr 2017 22:20:50: 106000000
INFO @ Thu, 13 Apr 2017 22:20:51: 107000000
INFO @ Thu, 13 Apr 2017 22:20:53: 108000000
INFO @ Thu, 13 Apr 2017 22:20:54: 109000000
INFO @ Thu, 13 Apr 2017 22:20:56: 110000000
INFO @ Thu, 13 Apr 2017 22:20:57: 111000000
INFO @ Thu, 13 Apr 2017 22:20:59: 112000000
INFO @ Thu, 13 Apr 2017 22:21:00: 113000000
INFO @ Thu, 13 Apr 2017 22:21:02: 114000000
INFO @ Thu, 13 Apr 2017 22:21:03: 115000000
INFO @ Thu, 13 Apr 2017 22:21:04: 116000000
INFO @ Thu, 13 Apr 2017 22:21:06: 117000000
INFO @ Thu, 13 Apr 2017 22:21:07: 118000000
INFO @ Thu, 13 Apr 2017 22:21:09: 119000000
INFO @ Thu, 13 Apr 2017 22:21:10: 120000000
INFO @ Thu, 13 Apr 2017 22:21:12: 121000000
INFO @ Thu, 13 Apr 2017 22:21:13: 122000000
INFO @ Thu, 13 Apr 2017 22:21:14: 123000000
INFO @ Thu, 13 Apr 2017 22:21:16: 124000000
INFO @ Thu, 13 Apr 2017 22:21:17: 125000000
INFO @ Thu, 13 Apr 2017 22:21:19: 126000000
INFO @ Thu, 13 Apr 2017 22:21:20: 127000000
INFO @ Thu, 13 Apr 2017 22:21:30: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:21:31: 1000000
INFO @ Thu, 13 Apr 2017 22:21:33: 2000000
INFO @ Thu, 13 Apr 2017 22:21:34: 3000000
INFO @ Thu, 13 Apr 2017 22:21:36: 4000000
INFO @ Thu, 13 Apr 2017 22:21:37: 5000000
INFO @ Thu, 13 Apr 2017 22:21:38: 6000000
INFO @ Thu, 13 Apr 2017 22:21:40: 7000000
INFO @ Thu, 13 Apr 2017 22:21:41: 8000000
INFO @ Thu, 13 Apr 2017 22:21:43: 9000000
INFO @ Thu, 13 Apr 2017 22:21:44: 10000000
INFO @ Thu, 13 Apr 2017 22:21:46: 11000000
INFO @ Thu, 13 Apr 2017 22:21:47: 12000000
INFO @ Thu, 13 Apr 2017 22:21:49: 13000000
INFO @ Thu, 13 Apr 2017 22:21:50: 14000000
INFO @ Thu, 13 Apr 2017 22:21:51: 15000000
INFO @ Thu, 13 Apr 2017 22:21:53: 16000000
INFO @ Thu, 13 Apr 2017 22:21:54: 17000000
INFO @ Thu, 13 Apr 2017 22:21:56: 18000000
INFO @ Thu, 13 Apr 2017 22:21:57: 19000000
INFO @ Thu, 13 Apr 2017 22:21:59: 20000000
INFO @ Thu, 13 Apr 2017 22:22:00: 21000000
INFO @ Thu, 13 Apr 2017 22:22:02: 22000000
INFO @ Thu, 13 Apr 2017 22:22:03: 23000000
INFO @ Thu, 13 Apr 2017 22:22:04: 24000000
INFO @ Thu, 13 Apr 2017 22:22:06: 25000000
INFO @ Thu, 13 Apr 2017 22:22:07: 26000000
INFO @ Thu, 13 Apr 2017 22:22:09: 27000000
INFO @ Thu, 13 Apr 2017 22:22:10: 28000000
INFO @ Thu, 13 Apr 2017 22:22:12: 29000000
INFO @ Thu, 13 Apr 2017 22:22:13: 30000000
INFO @ Thu, 13 Apr 2017 22:22:15: 31000000
INFO @ Thu, 13 Apr 2017 22:22:16: 32000000
INFO @ Thu, 13 Apr 2017 22:22:18: 33000000
INFO @ Thu, 13 Apr 2017 22:22:19: 34000000
INFO @ Thu, 13 Apr 2017 22:22:21: 35000000
INFO @ Thu, 13 Apr 2017 22:22:22: 36000000
INFO @ Thu, 13 Apr 2017 22:22:24: 37000000
INFO @ Thu, 13 Apr 2017 22:22:25: 38000000
INFO @ Thu, 13 Apr 2017 22:22:27: 39000000
INFO @ Thu, 13 Apr 2017 22:22:28: 40000000
INFO @ Thu, 13 Apr 2017 22:22:30: 41000000
INFO @ Thu, 13 Apr 2017 22:22:31: 42000000
INFO @ Thu, 13 Apr 2017 22:22:32: 43000000
INFO @ Thu, 13 Apr 2017 22:22:34: 44000000
INFO @ Thu, 13 Apr 2017 22:22:35: 45000000
INFO @ Thu, 13 Apr 2017 22:22:37: 46000000
INFO @ Thu, 13 Apr 2017 22:22:38: 47000000
INFO @ Thu, 13 Apr 2017 22:22:40: 48000000
INFO @ Thu, 13 Apr 2017 22:22:41: 49000000
INFO @ Thu, 13 Apr 2017 22:22:43: 50000000
INFO @ Thu, 13 Apr 2017 22:22:44: 51000000
INFO @ Thu, 13 Apr 2017 22:22:46: 52000000
INFO @ Thu, 13 Apr 2017 22:22:47: 53000000
INFO @ Thu, 13 Apr 2017 22:22:49: 54000000
INFO @ Thu, 13 Apr 2017 22:22:50: 55000000
INFO @ Thu, 13 Apr 2017 22:22:51: 56000000
INFO @ Thu, 13 Apr 2017 22:22:53: 57000000
INFO @ Thu, 13 Apr 2017 22:22:54: 58000000
INFO @ Thu, 13 Apr 2017 22:22:56: 59000000
INFO @ Thu, 13 Apr 2017 22:22:57: 60000000
INFO @ Thu, 13 Apr 2017 22:22:59: 61000000
INFO @ Thu, 13 Apr 2017 22:23:00: 62000000
INFO @ Thu, 13 Apr 2017 22:23:02: 63000000
INFO @ Thu, 13 Apr 2017 22:23:03: 64000000
INFO @ Thu, 13 Apr 2017 22:23:05: 65000000
INFO @ Thu, 13 Apr 2017 22:23:06: 66000000
INFO @ Thu, 13 Apr 2017 22:23:08: 67000000
INFO @ Thu, 13 Apr 2017 22:23:09: 68000000
INFO @ Thu, 13 Apr 2017 22:23:11: 69000000
INFO @ Thu, 13 Apr 2017 22:23:12: 70000000
INFO @ Thu, 13 Apr 2017 22:23:13: 71000000
INFO @ Thu, 13 Apr 2017 22:23:15: 72000000
INFO @ Thu, 13 Apr 2017 22:23:16: 73000000
INFO @ Thu, 13 Apr 2017 22:23:18: 74000000
INFO @ Thu, 13 Apr 2017 22:23:19: 75000000
INFO @ Thu, 13 Apr 2017 22:23:21: 76000000
INFO @ Thu, 13 Apr 2017 22:23:22: 77000000
INFO @ Thu, 13 Apr 2017 22:23:23: 78000000
INFO @ Thu, 13 Apr 2017 22:23:25: 79000000
INFO @ Thu, 13 Apr 2017 22:23:27: 80000000
INFO @ Thu, 13 Apr 2017 22:23:28: 81000000
INFO @ Thu, 13 Apr 2017 22:23:29: 82000000
INFO @ Thu, 13 Apr 2017 22:23:31: 83000000
INFO @ Thu, 13 Apr 2017 22:23:32: 84000000
INFO @ Thu, 13 Apr 2017 22:23:34: 85000000
INFO @ Thu, 13 Apr 2017 22:23:35: 86000000
INFO @ Thu, 13 Apr 2017 22:23:36: 87000000
INFO @ Thu, 13 Apr 2017 22:23:38: 88000000
INFO @ Thu, 13 Apr 2017 22:23:39: 89000000
INFO @ Thu, 13 Apr 2017 22:23:41: 90000000
INFO @ Thu, 13 Apr 2017 22:23:42: 91000000
INFO @ Thu, 13 Apr 2017 22:23:44: 92000000
INFO @ Thu, 13 Apr 2017 22:23:45: 93000000
INFO @ Thu, 13 Apr 2017 22:23:47: 94000000
INFO @ Thu, 13 Apr 2017 22:23:48: 95000000
INFO @ Thu, 13 Apr 2017 22:23:49: 96000000
INFO @ Thu, 13 Apr 2017 22:23:51: 97000000
INFO @ Thu, 13 Apr 2017 22:23:52: 98000000
INFO @ Thu, 13 Apr 2017 22:23:54: 99000000
INFO @ Thu, 13 Apr 2017 22:24:02: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:24:02: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:24:02: #1 total tags in treatment: 127505544
INFO @ Thu, 13 Apr 2017 22:24:02: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:24:02: #1 finished!
INFO @ Thu, 13 Apr 2017 22:24:02: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:24:02: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:24:02: #2 Use 235 as fragment length
INFO @ Thu, 13 Apr 2017 22:24:02: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:24:02: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:24:02: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 22:30:45: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 22:30:45: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 22:30:45: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 22:30:45: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 22:30:45: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 22:42:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 22:42:49: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 22:42:49: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 22:42:49: Done!
INFO @ Thu, 13 Apr 2017 22:42:51: Read and build treatment bedGraph...
INFO @ Thu, 13 Apr 2017 22:46:18: Read and build control bedGraph...
INFO @ Thu, 13 Apr 2017 22:48:50: Build scoreTrackII...
INFO @ Thu, 13 Apr 2017 22:50:30: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 13 Apr 2017 23:03:23: Write bedGraph of scores...
INFO @ Thu, 13 Apr 2017 23:13:42: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_FE.bdg'!
INFO @ Thu, 13 Apr 2017 23:34:19: Read and build treatment bedGraph...
INFO @ Thu, 13 Apr 2017 23:37:42: Read and build control bedGraph...
INFO @ Thu, 13 Apr 2017 23:40:09: Build scoreTrackII...
INFO @ Thu, 13 Apr 2017 23:41:44: Values in your input bedGraph files will be multiplied by 99.976272 ...
INFO @ Thu, 13 Apr 2017 23:54:22: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Thu, 13 Apr 2017 23:58:02: Write bedGraph of scores...
INFO @ Fri, 14 Apr 2017 00:04:59: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_ppois.bdg'!
|
Num | 7 | ID | task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_16 | Name | macs2 n/s rep1-pr1 | Thread | thread_Root | PID | 47043 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:18:07 | End | 2017-04-13 22:45:27 | Elapsed | 00:27:20 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
27233 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:18:32:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:18:32: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:18:32: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:18:34: 1000000
INFO @ Thu, 13 Apr 2017 22:18:36: 2000000
INFO @ Thu, 13 Apr 2017 22:18:38: 3000000
INFO @ Thu, 13 Apr 2017 22:18:40: 4000000
INFO @ Thu, 13 Apr 2017 22:18:42: 5000000
INFO @ Thu, 13 Apr 2017 22:18:44: 6000000
INFO @ Thu, 13 Apr 2017 22:18:46: 7000000
INFO @ Thu, 13 Apr 2017 22:18:47: 8000000
INFO @ Thu, 13 Apr 2017 22:18:49: 9000000
INFO @ Thu, 13 Apr 2017 22:18:51: 10000000
INFO @ Thu, 13 Apr 2017 22:18:53: 11000000
INFO @ Thu, 13 Apr 2017 22:18:55: 12000000
INFO @ Thu, 13 Apr 2017 22:18:57: 13000000
INFO @ Thu, 13 Apr 2017 22:18:59: 14000000
INFO @ Thu, 13 Apr 2017 22:19:01: 15000000
INFO @ Thu, 13 Apr 2017 22:19:03: 16000000
INFO @ Thu, 13 Apr 2017 22:19:05: 17000000
INFO @ Thu, 13 Apr 2017 22:19:07: 18000000
INFO @ Thu, 13 Apr 2017 22:19:08: 19000000
INFO @ Thu, 13 Apr 2017 22:19:10: 20000000
INFO @ Thu, 13 Apr 2017 22:19:12: 21000000
INFO @ Thu, 13 Apr 2017 22:19:14: 22000000
INFO @ Thu, 13 Apr 2017 22:19:16: 23000000
INFO @ Thu, 13 Apr 2017 22:19:18: 24000000
INFO @ Thu, 13 Apr 2017 22:19:20: 25000000
INFO @ Thu, 13 Apr 2017 22:19:22: 26000000
INFO @ Thu, 13 Apr 2017 22:19:24: 27000000
INFO @ Thu, 13 Apr 2017 22:19:26: 28000000
INFO @ Thu, 13 Apr 2017 22:19:27: 29000000
INFO @ Thu, 13 Apr 2017 22:19:29: 30000000
INFO @ Thu, 13 Apr 2017 22:19:31: 31000000
INFO @ Thu, 13 Apr 2017 22:19:33: 32000000
INFO @ Thu, 13 Apr 2017 22:19:35: 33000000
INFO @ Thu, 13 Apr 2017 22:19:37: 34000000
INFO @ Thu, 13 Apr 2017 22:19:40: 35000000
INFO @ Thu, 13 Apr 2017 22:19:42: 36000000
INFO @ Thu, 13 Apr 2017 22:19:44: 37000000
INFO @ Thu, 13 Apr 2017 22:19:46: 38000000
INFO @ Thu, 13 Apr 2017 22:19:48: 39000000
INFO @ Thu, 13 Apr 2017 22:19:50: 40000000
INFO @ Thu, 13 Apr 2017 22:19:52: 41000000
INFO @ Thu, 13 Apr 2017 22:19:54: 42000000
INFO @ Thu, 13 Apr 2017 22:19:56: 43000000
INFO @ Thu, 13 Apr 2017 22:19:58: 44000000
INFO @ Thu, 13 Apr 2017 22:20:00: 45000000
INFO @ Thu, 13 Apr 2017 22:20:01: 46000000
INFO @ Thu, 13 Apr 2017 22:20:03: 47000000
INFO @ Thu, 13 Apr 2017 22:20:05: 48000000
INFO @ Thu, 13 Apr 2017 22:20:07: 49000000
INFO @ Thu, 13 Apr 2017 22:20:09: 50000000
INFO @ Thu, 13 Apr 2017 22:20:11: 51000000
INFO @ Thu, 13 Apr 2017 22:20:13: 52000000
INFO @ Thu, 13 Apr 2017 22:20:15: 53000000
INFO @ Thu, 13 Apr 2017 22:20:17: 54000000
INFO @ Thu, 13 Apr 2017 22:20:19: 55000000
INFO @ Thu, 13 Apr 2017 22:20:21: 56000000
INFO @ Thu, 13 Apr 2017 22:20:23: 57000000
INFO @ Thu, 13 Apr 2017 22:20:25: 58000000
INFO @ Thu, 13 Apr 2017 22:20:26: 59000000
INFO @ Thu, 13 Apr 2017 22:20:28: 60000000
INFO @ Thu, 13 Apr 2017 22:20:30: 61000000
INFO @ Thu, 13 Apr 2017 22:20:32: 62000000
INFO @ Thu, 13 Apr 2017 22:20:34: 63000000
INFO @ Thu, 13 Apr 2017 22:20:41: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:20:43: 1000000
INFO @ Thu, 13 Apr 2017 22:20:45: 2000000
INFO @ Thu, 13 Apr 2017 22:20:47: 3000000
INFO @ Thu, 13 Apr 2017 22:20:49: 4000000
INFO @ Thu, 13 Apr 2017 22:20:51: 5000000
INFO @ Thu, 13 Apr 2017 22:20:53: 6000000
INFO @ Thu, 13 Apr 2017 22:20:55: 7000000
INFO @ Thu, 13 Apr 2017 22:20:57: 8000000
INFO @ Thu, 13 Apr 2017 22:20:59: 9000000
INFO @ Thu, 13 Apr 2017 22:21:01: 10000000
INFO @ Thu, 13 Apr 2017 22:21:03: 11000000
INFO @ Thu, 13 Apr 2017 22:21:05: 12000000
INFO @ Thu, 13 Apr 2017 22:21:07: 13000000
INFO @ Thu, 13 Apr 2017 22:21:08: 14000000
INFO @ Thu, 13 Apr 2017 22:21:10: 15000000
INFO @ Thu, 13 Apr 2017 22:21:12: 16000000
INFO @ Thu, 13 Apr 2017 22:21:14: 17000000
INFO @ Thu, 13 Apr 2017 22:21:16: 18000000
INFO @ Thu, 13 Apr 2017 22:21:18: 19000000
INFO @ Thu, 13 Apr 2017 22:21:20: 20000000
INFO @ Thu, 13 Apr 2017 22:21:22: 21000000
INFO @ Thu, 13 Apr 2017 22:21:24: 22000000
INFO @ Thu, 13 Apr 2017 22:21:26: 23000000
INFO @ Thu, 13 Apr 2017 22:21:27: 24000000
INFO @ Thu, 13 Apr 2017 22:21:29: 25000000
INFO @ Thu, 13 Apr 2017 22:21:31: 26000000
INFO @ Thu, 13 Apr 2017 22:21:33: 27000000
INFO @ Thu, 13 Apr 2017 22:21:35: 28000000
INFO @ Thu, 13 Apr 2017 22:21:37: 29000000
INFO @ Thu, 13 Apr 2017 22:21:40: 30000000
INFO @ Thu, 13 Apr 2017 22:21:42: 31000000
INFO @ Thu, 13 Apr 2017 22:21:44: 32000000
INFO @ Thu, 13 Apr 2017 22:21:46: 33000000
INFO @ Thu, 13 Apr 2017 22:21:48: 34000000
INFO @ Thu, 13 Apr 2017 22:21:50: 35000000
INFO @ Thu, 13 Apr 2017 22:21:52: 36000000
INFO @ Thu, 13 Apr 2017 22:21:54: 37000000
INFO @ Thu, 13 Apr 2017 22:21:55: 38000000
INFO @ Thu, 13 Apr 2017 22:21:57: 39000000
INFO @ Thu, 13 Apr 2017 22:21:59: 40000000
INFO @ Thu, 13 Apr 2017 22:22:01: 41000000
INFO @ Thu, 13 Apr 2017 22:22:03: 42000000
INFO @ Thu, 13 Apr 2017 22:22:05: 43000000
INFO @ Thu, 13 Apr 2017 22:22:07: 44000000
INFO @ Thu, 13 Apr 2017 22:22:09: 45000000
INFO @ Thu, 13 Apr 2017 22:22:11: 46000000
INFO @ Thu, 13 Apr 2017 22:22:13: 47000000
INFO @ Thu, 13 Apr 2017 22:22:15: 48000000
INFO @ Thu, 13 Apr 2017 22:22:17: 49000000
INFO @ Thu, 13 Apr 2017 22:22:19: 50000000
INFO @ Thu, 13 Apr 2017 22:22:20: 51000000
INFO @ Thu, 13 Apr 2017 22:22:22: 52000000
INFO @ Thu, 13 Apr 2017 22:22:24: 53000000
INFO @ Thu, 13 Apr 2017 22:22:26: 54000000
INFO @ Thu, 13 Apr 2017 22:22:28: 55000000
INFO @ Thu, 13 Apr 2017 22:22:30: 56000000
INFO @ Thu, 13 Apr 2017 22:22:32: 57000000
INFO @ Thu, 13 Apr 2017 22:22:34: 58000000
INFO @ Thu, 13 Apr 2017 22:22:36: 59000000
INFO @ Thu, 13 Apr 2017 22:22:38: 60000000
INFO @ Thu, 13 Apr 2017 22:22:40: 61000000
INFO @ Thu, 13 Apr 2017 22:22:42: 62000000
INFO @ Thu, 13 Apr 2017 22:22:44: 63000000
INFO @ Thu, 13 Apr 2017 22:22:46: 64000000
INFO @ Thu, 13 Apr 2017 22:22:47: 65000000
INFO @ Thu, 13 Apr 2017 22:22:49: 66000000
INFO @ Thu, 13 Apr 2017 22:22:51: 67000000
INFO @ Thu, 13 Apr 2017 22:22:53: 68000000
INFO @ Thu, 13 Apr 2017 22:22:55: 69000000
INFO @ Thu, 13 Apr 2017 22:22:57: 70000000
INFO @ Thu, 13 Apr 2017 22:22:59: 71000000
INFO @ Thu, 13 Apr 2017 22:23:01: 72000000
INFO @ Thu, 13 Apr 2017 22:23:03: 73000000
INFO @ Thu, 13 Apr 2017 22:23:05: 74000000
INFO @ Thu, 13 Apr 2017 22:23:07: 75000000
INFO @ Thu, 13 Apr 2017 22:23:09: 76000000
INFO @ Thu, 13 Apr 2017 22:23:11: 77000000
INFO @ Thu, 13 Apr 2017 22:23:13: 78000000
INFO @ Thu, 13 Apr 2017 22:23:15: 79000000
INFO @ Thu, 13 Apr 2017 22:23:17: 80000000
INFO @ Thu, 13 Apr 2017 22:23:19: 81000000
INFO @ Thu, 13 Apr 2017 22:23:20: 82000000
INFO @ Thu, 13 Apr 2017 22:23:22: 83000000
INFO @ Thu, 13 Apr 2017 22:23:24: 84000000
INFO @ Thu, 13 Apr 2017 22:23:26: 85000000
INFO @ Thu, 13 Apr 2017 22:23:28: 86000000
INFO @ Thu, 13 Apr 2017 22:23:30: 87000000
INFO @ Thu, 13 Apr 2017 22:23:32: 88000000
INFO @ Thu, 13 Apr 2017 22:23:34: 89000000
INFO @ Thu, 13 Apr 2017 22:23:36: 90000000
INFO @ Thu, 13 Apr 2017 22:23:38: 91000000
INFO @ Thu, 13 Apr 2017 22:23:40: 92000000
INFO @ Thu, 13 Apr 2017 22:23:42: 93000000
INFO @ Thu, 13 Apr 2017 22:23:44: 94000000
INFO @ Thu, 13 Apr 2017 22:23:46: 95000000
INFO @ Thu, 13 Apr 2017 22:23:48: 96000000
INFO @ Thu, 13 Apr 2017 22:23:50: 97000000
INFO @ Thu, 13 Apr 2017 22:23:51: 98000000
INFO @ Thu, 13 Apr 2017 22:23:53: 99000000
INFO @ Thu, 13 Apr 2017 22:24:04: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:24:04: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:24:04: #1 total tags in treatment: 63752772
INFO @ Thu, 13 Apr 2017 22:24:04: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:24:04: #1 finished!
INFO @ Thu, 13 Apr 2017 22:24:04: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:24:04: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:24:04: #2 Use 235 as fragment length
INFO @ Thu, 13 Apr 2017 22:24:04: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:24:04: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:24:04: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 22:31:49: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 22:31:49: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 22:31:49: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 22:31:49: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 22:31:49: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 22:45:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 22:45:22: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 22:45:23: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 22:45:23: Done!
|
Num | 8 | ID | task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_17 | Name | macs2 n/s rep1-pr2 | Thread | thread_Root | PID | 47044 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:45:30 | End | 2017-04-13 23:05:33 | Elapsed | 00:20:03 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
1046 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:45:46:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:45:46: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:45:46: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:45:48: 1000000
INFO @ Thu, 13 Apr 2017 22:45:50: 2000000
INFO @ Thu, 13 Apr 2017 22:45:52: 3000000
INFO @ Thu, 13 Apr 2017 22:45:53: 4000000
INFO @ Thu, 13 Apr 2017 22:45:55: 5000000
INFO @ Thu, 13 Apr 2017 22:45:57: 6000000
INFO @ Thu, 13 Apr 2017 22:45:59: 7000000
INFO @ Thu, 13 Apr 2017 22:46:00: 8000000
INFO @ Thu, 13 Apr 2017 22:46:02: 9000000
INFO @ Thu, 13 Apr 2017 22:46:04: 10000000
INFO @ Thu, 13 Apr 2017 22:46:05: 11000000
INFO @ Thu, 13 Apr 2017 22:46:07: 12000000
INFO @ Thu, 13 Apr 2017 22:46:09: 13000000
INFO @ Thu, 13 Apr 2017 22:46:10: 14000000
INFO @ Thu, 13 Apr 2017 22:46:12: 15000000
INFO @ Thu, 13 Apr 2017 22:46:13: 16000000
INFO @ Thu, 13 Apr 2017 22:46:15: 17000000
INFO @ Thu, 13 Apr 2017 22:46:16: 18000000
INFO @ Thu, 13 Apr 2017 22:46:18: 19000000
INFO @ Thu, 13 Apr 2017 22:46:20: 20000000
INFO @ Thu, 13 Apr 2017 22:46:22: 21000000
INFO @ Thu, 13 Apr 2017 22:46:23: 22000000
INFO @ Thu, 13 Apr 2017 22:46:25: 23000000
INFO @ Thu, 13 Apr 2017 22:46:27: 24000000
INFO @ Thu, 13 Apr 2017 22:46:29: 25000000
INFO @ Thu, 13 Apr 2017 22:46:30: 26000000
INFO @ Thu, 13 Apr 2017 22:46:32: 27000000
INFO @ Thu, 13 Apr 2017 22:46:34: 28000000
INFO @ Thu, 13 Apr 2017 22:46:36: 29000000
INFO @ Thu, 13 Apr 2017 22:46:38: 30000000
INFO @ Thu, 13 Apr 2017 22:46:40: 31000000
INFO @ Thu, 13 Apr 2017 22:46:42: 32000000
INFO @ Thu, 13 Apr 2017 22:46:43: 33000000
INFO @ Thu, 13 Apr 2017 22:46:45: 34000000
INFO @ Thu, 13 Apr 2017 22:46:47: 35000000
INFO @ Thu, 13 Apr 2017 22:46:49: 36000000
INFO @ Thu, 13 Apr 2017 22:46:50: 37000000
INFO @ Thu, 13 Apr 2017 22:46:52: 38000000
INFO @ Thu, 13 Apr 2017 22:46:54: 39000000
INFO @ Thu, 13 Apr 2017 22:46:56: 40000000
INFO @ Thu, 13 Apr 2017 22:46:57: 41000000
INFO @ Thu, 13 Apr 2017 22:46:59: 42000000
INFO @ Thu, 13 Apr 2017 22:47:01: 43000000
INFO @ Thu, 13 Apr 2017 22:47:03: 44000000
INFO @ Thu, 13 Apr 2017 22:47:05: 45000000
INFO @ Thu, 13 Apr 2017 22:47:07: 46000000
INFO @ Thu, 13 Apr 2017 22:47:08: 47000000
INFO @ Thu, 13 Apr 2017 22:47:11: 48000000
INFO @ Thu, 13 Apr 2017 22:47:12: 49000000
INFO @ Thu, 13 Apr 2017 22:47:14: 50000000
INFO @ Thu, 13 Apr 2017 22:47:16: 51000000
INFO @ Thu, 13 Apr 2017 22:47:17: 52000000
INFO @ Thu, 13 Apr 2017 22:47:19: 53000000
INFO @ Thu, 13 Apr 2017 22:47:20: 54000000
INFO @ Thu, 13 Apr 2017 22:47:22: 55000000
INFO @ Thu, 13 Apr 2017 22:47:24: 56000000
INFO @ Thu, 13 Apr 2017 22:47:26: 57000000
INFO @ Thu, 13 Apr 2017 22:47:28: 58000000
INFO @ Thu, 13 Apr 2017 22:47:30: 59000000
INFO @ Thu, 13 Apr 2017 22:47:31: 60000000
INFO @ Thu, 13 Apr 2017 22:47:32: 61000000
INFO @ Thu, 13 Apr 2017 22:47:34: 62000000
INFO @ Thu, 13 Apr 2017 22:47:35: 63000000
INFO @ Thu, 13 Apr 2017 22:47:41: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:47:42: 1000000
INFO @ Thu, 13 Apr 2017 22:47:44: 2000000
INFO @ Thu, 13 Apr 2017 22:47:45: 3000000
INFO @ Thu, 13 Apr 2017 22:47:47: 4000000
INFO @ Thu, 13 Apr 2017 22:47:48: 5000000
INFO @ Thu, 13 Apr 2017 22:47:50: 6000000
INFO @ Thu, 13 Apr 2017 22:47:51: 7000000
INFO @ Thu, 13 Apr 2017 22:47:53: 8000000
INFO @ Thu, 13 Apr 2017 22:47:54: 9000000
INFO @ Thu, 13 Apr 2017 22:47:56: 10000000
INFO @ Thu, 13 Apr 2017 22:47:57: 11000000
INFO @ Thu, 13 Apr 2017 22:47:59: 12000000
INFO @ Thu, 13 Apr 2017 22:48:00: 13000000
INFO @ Thu, 13 Apr 2017 22:48:02: 14000000
INFO @ Thu, 13 Apr 2017 22:48:03: 15000000
INFO @ Thu, 13 Apr 2017 22:48:04: 16000000
INFO @ Thu, 13 Apr 2017 22:48:06: 17000000
INFO @ Thu, 13 Apr 2017 22:48:07: 18000000
INFO @ Thu, 13 Apr 2017 22:48:09: 19000000
INFO @ Thu, 13 Apr 2017 22:48:10: 20000000
INFO @ Thu, 13 Apr 2017 22:48:12: 21000000
INFO @ Thu, 13 Apr 2017 22:48:13: 22000000
INFO @ Thu, 13 Apr 2017 22:48:15: 23000000
INFO @ Thu, 13 Apr 2017 22:48:16: 24000000
INFO @ Thu, 13 Apr 2017 22:48:17: 25000000
INFO @ Thu, 13 Apr 2017 22:48:19: 26000000
INFO @ Thu, 13 Apr 2017 22:48:20: 27000000
INFO @ Thu, 13 Apr 2017 22:48:22: 28000000
INFO @ Thu, 13 Apr 2017 22:48:23: 29000000
INFO @ Thu, 13 Apr 2017 22:48:25: 30000000
INFO @ Thu, 13 Apr 2017 22:48:26: 31000000
INFO @ Thu, 13 Apr 2017 22:48:28: 32000000
INFO @ Thu, 13 Apr 2017 22:48:29: 33000000
INFO @ Thu, 13 Apr 2017 22:48:31: 34000000
INFO @ Thu, 13 Apr 2017 22:48:32: 35000000
INFO @ Thu, 13 Apr 2017 22:48:34: 36000000
INFO @ Thu, 13 Apr 2017 22:48:35: 37000000
INFO @ Thu, 13 Apr 2017 22:48:37: 38000000
INFO @ Thu, 13 Apr 2017 22:48:38: 39000000
INFO @ Thu, 13 Apr 2017 22:48:40: 40000000
INFO @ Thu, 13 Apr 2017 22:48:41: 41000000
INFO @ Thu, 13 Apr 2017 22:48:42: 42000000
INFO @ Thu, 13 Apr 2017 22:48:44: 43000000
INFO @ Thu, 13 Apr 2017 22:48:45: 44000000
INFO @ Thu, 13 Apr 2017 22:48:47: 45000000
INFO @ Thu, 13 Apr 2017 22:48:48: 46000000
INFO @ Thu, 13 Apr 2017 22:48:50: 47000000
INFO @ Thu, 13 Apr 2017 22:48:51: 48000000
INFO @ Thu, 13 Apr 2017 22:48:53: 49000000
INFO @ Thu, 13 Apr 2017 22:48:54: 50000000
INFO @ Thu, 13 Apr 2017 22:48:56: 51000000
INFO @ Thu, 13 Apr 2017 22:48:57: 52000000
INFO @ Thu, 13 Apr 2017 22:48:59: 53000000
INFO @ Thu, 13 Apr 2017 22:49:00: 54000000
INFO @ Thu, 13 Apr 2017 22:49:02: 55000000
INFO @ Thu, 13 Apr 2017 22:49:03: 56000000
INFO @ Thu, 13 Apr 2017 22:49:04: 57000000
INFO @ Thu, 13 Apr 2017 22:49:06: 58000000
INFO @ Thu, 13 Apr 2017 22:49:07: 59000000
INFO @ Thu, 13 Apr 2017 22:49:09: 60000000
INFO @ Thu, 13 Apr 2017 22:49:10: 61000000
INFO @ Thu, 13 Apr 2017 22:49:12: 62000000
INFO @ Thu, 13 Apr 2017 22:49:13: 63000000
INFO @ Thu, 13 Apr 2017 22:49:14: 64000000
INFO @ Thu, 13 Apr 2017 22:49:16: 65000000
INFO @ Thu, 13 Apr 2017 22:49:17: 66000000
INFO @ Thu, 13 Apr 2017 22:49:19: 67000000
INFO @ Thu, 13 Apr 2017 22:49:20: 68000000
INFO @ Thu, 13 Apr 2017 22:49:22: 69000000
INFO @ Thu, 13 Apr 2017 22:49:23: 70000000
INFO @ Thu, 13 Apr 2017 22:49:25: 71000000
INFO @ Thu, 13 Apr 2017 22:49:26: 72000000
INFO @ Thu, 13 Apr 2017 22:49:28: 73000000
INFO @ Thu, 13 Apr 2017 22:49:29: 74000000
INFO @ Thu, 13 Apr 2017 22:49:31: 75000000
INFO @ Thu, 13 Apr 2017 22:49:32: 76000000
INFO @ Thu, 13 Apr 2017 22:49:33: 77000000
INFO @ Thu, 13 Apr 2017 22:49:35: 78000000
INFO @ Thu, 13 Apr 2017 22:49:36: 79000000
INFO @ Thu, 13 Apr 2017 22:49:38: 80000000
INFO @ Thu, 13 Apr 2017 22:49:39: 81000000
INFO @ Thu, 13 Apr 2017 22:49:41: 82000000
INFO @ Thu, 13 Apr 2017 22:49:42: 83000000
INFO @ Thu, 13 Apr 2017 22:49:44: 84000000
INFO @ Thu, 13 Apr 2017 22:49:45: 85000000
INFO @ Thu, 13 Apr 2017 22:49:47: 86000000
INFO @ Thu, 13 Apr 2017 22:49:48: 87000000
INFO @ Thu, 13 Apr 2017 22:49:49: 88000000
INFO @ Thu, 13 Apr 2017 22:49:51: 89000000
INFO @ Thu, 13 Apr 2017 22:49:52: 90000000
INFO @ Thu, 13 Apr 2017 22:49:54: 91000000
INFO @ Thu, 13 Apr 2017 22:49:55: 92000000
INFO @ Thu, 13 Apr 2017 22:49:57: 93000000
INFO @ Thu, 13 Apr 2017 22:49:58: 94000000
INFO @ Thu, 13 Apr 2017 22:50:00: 95000000
INFO @ Thu, 13 Apr 2017 22:50:01: 96000000
INFO @ Thu, 13 Apr 2017 22:50:02: 97000000
INFO @ Thu, 13 Apr 2017 22:50:04: 98000000
INFO @ Thu, 13 Apr 2017 22:50:05: 99000000
INFO @ Thu, 13 Apr 2017 22:50:14: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:50:14: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:50:14: #1 total tags in treatment: 63752772
INFO @ Thu, 13 Apr 2017 22:50:14: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:50:14: #1 finished!
INFO @ Thu, 13 Apr 2017 22:50:14: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:50:14: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:50:14: #2 Use 235 as fragment length
INFO @ Thu, 13 Apr 2017 22:50:14: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:50:14: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:50:14: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 22:55:57: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 22:55:57: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 22:55:57: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 22:55:57: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 22:55:57: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 23:05:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 23:05:30: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 23:05:30: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 23:05:30: Done!
|
Num | 9 | ID | task.callpeak_macs2.macs2_n_s_rep2.line_66.id_18 | Name | macs2 n/s rep2 | Thread | thread_Root | PID | 47045 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:50:41 | End | 2017-04-14 00:35:28 | Elapsed | 01:44:46 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2 -o "ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2 -o "ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
18621 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:51:01:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:51:01: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:51:01: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:51:03: 1000000
INFO @ Thu, 13 Apr 2017 22:51:04: 2000000
INFO @ Thu, 13 Apr 2017 22:51:06: 3000000
INFO @ Thu, 13 Apr 2017 22:51:07: 4000000
INFO @ Thu, 13 Apr 2017 22:51:09: 5000000
INFO @ Thu, 13 Apr 2017 22:51:10: 6000000
INFO @ Thu, 13 Apr 2017 22:51:12: 7000000
INFO @ Thu, 13 Apr 2017 22:51:13: 8000000
INFO @ Thu, 13 Apr 2017 22:51:15: 9000000
INFO @ Thu, 13 Apr 2017 22:51:17: 10000000
INFO @ Thu, 13 Apr 2017 22:51:18: 11000000
INFO @ Thu, 13 Apr 2017 22:51:20: 12000000
INFO @ Thu, 13 Apr 2017 22:51:22: 13000000
INFO @ Thu, 13 Apr 2017 22:51:24: 14000000
INFO @ Thu, 13 Apr 2017 22:51:25: 15000000
INFO @ Thu, 13 Apr 2017 22:51:27: 16000000
INFO @ Thu, 13 Apr 2017 22:51:29: 17000000
INFO @ Thu, 13 Apr 2017 22:51:31: 18000000
INFO @ Thu, 13 Apr 2017 22:51:32: 19000000
INFO @ Thu, 13 Apr 2017 22:51:34: 20000000
INFO @ Thu, 13 Apr 2017 22:51:36: 21000000
INFO @ Thu, 13 Apr 2017 22:51:37: 22000000
INFO @ Thu, 13 Apr 2017 22:51:39: 23000000
INFO @ Thu, 13 Apr 2017 22:51:40: 24000000
INFO @ Thu, 13 Apr 2017 22:51:42: 25000000
INFO @ Thu, 13 Apr 2017 22:51:44: 26000000
INFO @ Thu, 13 Apr 2017 22:51:46: 27000000
INFO @ Thu, 13 Apr 2017 22:51:47: 28000000
INFO @ Thu, 13 Apr 2017 22:51:49: 29000000
INFO @ Thu, 13 Apr 2017 22:51:51: 30000000
INFO @ Thu, 13 Apr 2017 22:51:52: 31000000
INFO @ Thu, 13 Apr 2017 22:51:54: 32000000
INFO @ Thu, 13 Apr 2017 22:51:56: 33000000
INFO @ Thu, 13 Apr 2017 22:51:57: 34000000
INFO @ Thu, 13 Apr 2017 22:51:59: 35000000
INFO @ Thu, 13 Apr 2017 22:52:01: 36000000
INFO @ Thu, 13 Apr 2017 22:52:02: 37000000
INFO @ Thu, 13 Apr 2017 22:52:04: 38000000
INFO @ Thu, 13 Apr 2017 22:52:05: 39000000
INFO @ Thu, 13 Apr 2017 22:52:07: 40000000
INFO @ Thu, 13 Apr 2017 22:52:09: 41000000
INFO @ Thu, 13 Apr 2017 22:52:10: 42000000
INFO @ Thu, 13 Apr 2017 22:52:12: 43000000
INFO @ Thu, 13 Apr 2017 22:52:14: 44000000
INFO @ Thu, 13 Apr 2017 22:52:15: 45000000
INFO @ Thu, 13 Apr 2017 22:52:17: 46000000
INFO @ Thu, 13 Apr 2017 22:52:19: 47000000
INFO @ Thu, 13 Apr 2017 22:52:20: 48000000
INFO @ Thu, 13 Apr 2017 22:52:22: 49000000
INFO @ Thu, 13 Apr 2017 22:52:23: 50000000
INFO @ Thu, 13 Apr 2017 22:52:25: 51000000
INFO @ Thu, 13 Apr 2017 22:52:26: 52000000
INFO @ Thu, 13 Apr 2017 22:52:28: 53000000
INFO @ Thu, 13 Apr 2017 22:52:29: 54000000
INFO @ Thu, 13 Apr 2017 22:52:31: 55000000
INFO @ Thu, 13 Apr 2017 22:52:32: 56000000
INFO @ Thu, 13 Apr 2017 22:52:34: 57000000
INFO @ Thu, 13 Apr 2017 22:52:35: 58000000
INFO @ Thu, 13 Apr 2017 22:52:37: 59000000
INFO @ Thu, 13 Apr 2017 22:52:38: 60000000
INFO @ Thu, 13 Apr 2017 22:52:40: 61000000
INFO @ Thu, 13 Apr 2017 22:52:41: 62000000
INFO @ Thu, 13 Apr 2017 22:52:42: 63000000
INFO @ Thu, 13 Apr 2017 22:52:44: 64000000
INFO @ Thu, 13 Apr 2017 22:52:45: 65000000
INFO @ Thu, 13 Apr 2017 22:52:47: 66000000
INFO @ Thu, 13 Apr 2017 22:52:48: 67000000
INFO @ Thu, 13 Apr 2017 22:52:50: 68000000
INFO @ Thu, 13 Apr 2017 22:52:51: 69000000
INFO @ Thu, 13 Apr 2017 22:52:53: 70000000
INFO @ Thu, 13 Apr 2017 22:52:54: 71000000
INFO @ Thu, 13 Apr 2017 22:52:56: 72000000
INFO @ Thu, 13 Apr 2017 22:52:57: 73000000
INFO @ Thu, 13 Apr 2017 22:52:59: 74000000
INFO @ Thu, 13 Apr 2017 22:53:00: 75000000
INFO @ Thu, 13 Apr 2017 22:53:02: 76000000
INFO @ Thu, 13 Apr 2017 22:53:03: 77000000
INFO @ Thu, 13 Apr 2017 22:53:05: 78000000
INFO @ Thu, 13 Apr 2017 22:53:06: 79000000
INFO @ Thu, 13 Apr 2017 22:53:08: 80000000
INFO @ Thu, 13 Apr 2017 22:53:09: 81000000
INFO @ Thu, 13 Apr 2017 22:53:11: 82000000
INFO @ Thu, 13 Apr 2017 22:53:12: 83000000
INFO @ Thu, 13 Apr 2017 22:53:14: 84000000
INFO @ Thu, 13 Apr 2017 22:53:15: 85000000
INFO @ Thu, 13 Apr 2017 22:53:17: 86000000
INFO @ Thu, 13 Apr 2017 22:53:18: 87000000
INFO @ Thu, 13 Apr 2017 22:53:20: 88000000
INFO @ Thu, 13 Apr 2017 22:53:21: 89000000
INFO @ Thu, 13 Apr 2017 22:53:23: 90000000
INFO @ Thu, 13 Apr 2017 22:53:24: 91000000
INFO @ Thu, 13 Apr 2017 22:53:25: 92000000
INFO @ Thu, 13 Apr 2017 22:53:32: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:53:34: 1000000
INFO @ Thu, 13 Apr 2017 22:53:35: 2000000
INFO @ Thu, 13 Apr 2017 22:53:37: 3000000
INFO @ Thu, 13 Apr 2017 22:53:38: 4000000
INFO @ Thu, 13 Apr 2017 22:53:40: 5000000
INFO @ Thu, 13 Apr 2017 22:53:41: 6000000
INFO @ Thu, 13 Apr 2017 22:53:43: 7000000
INFO @ Thu, 13 Apr 2017 22:53:44: 8000000
INFO @ Thu, 13 Apr 2017 22:53:46: 9000000
INFO @ Thu, 13 Apr 2017 22:53:47: 10000000
INFO @ Thu, 13 Apr 2017 22:53:48: 11000000
INFO @ Thu, 13 Apr 2017 22:53:50: 12000000
INFO @ Thu, 13 Apr 2017 22:53:51: 13000000
INFO @ Thu, 13 Apr 2017 22:53:53: 14000000
INFO @ Thu, 13 Apr 2017 22:53:54: 15000000
INFO @ Thu, 13 Apr 2017 22:53:56: 16000000
INFO @ Thu, 13 Apr 2017 22:53:57: 17000000
INFO @ Thu, 13 Apr 2017 22:53:59: 18000000
INFO @ Thu, 13 Apr 2017 22:54:00: 19000000
INFO @ Thu, 13 Apr 2017 22:54:02: 20000000
INFO @ Thu, 13 Apr 2017 22:54:03: 21000000
INFO @ Thu, 13 Apr 2017 22:54:05: 22000000
INFO @ Thu, 13 Apr 2017 22:54:06: 23000000
INFO @ Thu, 13 Apr 2017 22:54:08: 24000000
INFO @ Thu, 13 Apr 2017 22:54:09: 25000000
INFO @ Thu, 13 Apr 2017 22:54:11: 26000000
INFO @ Thu, 13 Apr 2017 22:54:12: 27000000
INFO @ Thu, 13 Apr 2017 22:54:14: 28000000
INFO @ Thu, 13 Apr 2017 22:54:15: 29000000
INFO @ Thu, 13 Apr 2017 22:54:17: 30000000
INFO @ Thu, 13 Apr 2017 22:54:18: 31000000
INFO @ Thu, 13 Apr 2017 22:54:20: 32000000
INFO @ Thu, 13 Apr 2017 22:54:21: 33000000
INFO @ Thu, 13 Apr 2017 22:54:23: 34000000
INFO @ Thu, 13 Apr 2017 22:54:24: 35000000
INFO @ Thu, 13 Apr 2017 22:54:26: 36000000
INFO @ Thu, 13 Apr 2017 22:54:27: 37000000
INFO @ Thu, 13 Apr 2017 22:54:29: 38000000
INFO @ Thu, 13 Apr 2017 22:54:30: 39000000
INFO @ Thu, 13 Apr 2017 22:54:32: 40000000
INFO @ Thu, 13 Apr 2017 22:54:33: 41000000
INFO @ Thu, 13 Apr 2017 22:54:35: 42000000
INFO @ Thu, 13 Apr 2017 22:54:36: 43000000
INFO @ Thu, 13 Apr 2017 22:54:37: 44000000
INFO @ Thu, 13 Apr 2017 22:54:39: 45000000
INFO @ Thu, 13 Apr 2017 22:54:40: 46000000
INFO @ Thu, 13 Apr 2017 22:54:42: 47000000
INFO @ Thu, 13 Apr 2017 22:54:43: 48000000
INFO @ Thu, 13 Apr 2017 22:54:45: 49000000
INFO @ Thu, 13 Apr 2017 22:54:46: 50000000
INFO @ Thu, 13 Apr 2017 22:54:48: 51000000
INFO @ Thu, 13 Apr 2017 22:54:49: 52000000
INFO @ Thu, 13 Apr 2017 22:54:51: 53000000
INFO @ Thu, 13 Apr 2017 22:54:52: 54000000
INFO @ Thu, 13 Apr 2017 22:54:54: 55000000
INFO @ Thu, 13 Apr 2017 22:54:55: 56000000
INFO @ Thu, 13 Apr 2017 22:54:57: 57000000
INFO @ Thu, 13 Apr 2017 22:54:58: 58000000
INFO @ Thu, 13 Apr 2017 22:55:00: 59000000
INFO @ Thu, 13 Apr 2017 22:55:01: 60000000
INFO @ Thu, 13 Apr 2017 22:55:03: 61000000
INFO @ Thu, 13 Apr 2017 22:55:04: 62000000
INFO @ Thu, 13 Apr 2017 22:55:06: 63000000
INFO @ Thu, 13 Apr 2017 22:55:07: 64000000
INFO @ Thu, 13 Apr 2017 22:55:09: 65000000
INFO @ Thu, 13 Apr 2017 22:55:10: 66000000
INFO @ Thu, 13 Apr 2017 22:55:12: 67000000
INFO @ Thu, 13 Apr 2017 22:55:13: 68000000
INFO @ Thu, 13 Apr 2017 22:55:15: 69000000
INFO @ Thu, 13 Apr 2017 22:55:16: 70000000
INFO @ Thu, 13 Apr 2017 22:55:18: 71000000
INFO @ Thu, 13 Apr 2017 22:55:19: 72000000
INFO @ Thu, 13 Apr 2017 22:55:20: 73000000
INFO @ Thu, 13 Apr 2017 22:55:22: 74000000
INFO @ Thu, 13 Apr 2017 22:55:23: 75000000
INFO @ Thu, 13 Apr 2017 22:55:25: 76000000
INFO @ Thu, 13 Apr 2017 22:55:26: 77000000
INFO @ Thu, 13 Apr 2017 22:55:28: 78000000
INFO @ Thu, 13 Apr 2017 22:55:29: 79000000
INFO @ Thu, 13 Apr 2017 22:55:31: 80000000
INFO @ Thu, 13 Apr 2017 22:55:32: 81000000
INFO @ Thu, 13 Apr 2017 22:55:34: 82000000
INFO @ Thu, 13 Apr 2017 22:55:35: 83000000
INFO @ Thu, 13 Apr 2017 22:55:37: 84000000
INFO @ Thu, 13 Apr 2017 22:55:38: 85000000
INFO @ Thu, 13 Apr 2017 22:55:40: 86000000
INFO @ Thu, 13 Apr 2017 22:55:41: 87000000
INFO @ Thu, 13 Apr 2017 22:55:42: 88000000
INFO @ Thu, 13 Apr 2017 22:55:44: 89000000
INFO @ Thu, 13 Apr 2017 22:55:45: 90000000
INFO @ Thu, 13 Apr 2017 22:55:47: 91000000
INFO @ Thu, 13 Apr 2017 22:55:48: 92000000
INFO @ Thu, 13 Apr 2017 22:55:50: 93000000
INFO @ Thu, 13 Apr 2017 22:55:51: 94000000
INFO @ Thu, 13 Apr 2017 22:55:53: 95000000
INFO @ Thu, 13 Apr 2017 22:55:54: 96000000
INFO @ Thu, 13 Apr 2017 22:55:56: 97000000
INFO @ Thu, 13 Apr 2017 22:55:57: 98000000
INFO @ Thu, 13 Apr 2017 22:55:59: 99000000
INFO @ Thu, 13 Apr 2017 22:56:07: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:56:07: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:56:07: #1 total tags in treatment: 92229774
INFO @ Thu, 13 Apr 2017 22:56:07: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:56:07: #1 finished!
INFO @ Thu, 13 Apr 2017 22:56:07: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:56:07: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:56:07: #2 Use 240 as fragment length
INFO @ Thu, 13 Apr 2017 22:56:07: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:56:07: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:56:07: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 23:02:28: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 23:02:28: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 23:02:28: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 23:02:28: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 23:02:28: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 23:13:24: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 23:13:24: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 23:13:24: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 23:13:24: Done!
INFO @ Thu, 13 Apr 2017 23:13:27: Read and build treatment bedGraph...
INFO @ Thu, 13 Apr 2017 23:15:55: Read and build control bedGraph...
INFO @ Thu, 13 Apr 2017 23:18:22: Build scoreTrackII...
INFO @ Thu, 13 Apr 2017 23:19:41: Calculate scores comparing treatment and control by 'FE'...
INFO @ Thu, 13 Apr 2017 23:30:13: Write bedGraph of scores...
INFO @ Thu, 13 Apr 2017 23:38:27: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_FE.bdg'!
INFO @ Thu, 13 Apr 2017 23:55:42: Read and build treatment bedGraph...
INFO @ Thu, 13 Apr 2017 23:58:10: Read and build control bedGraph...
INFO @ Fri, 14 Apr 2017 00:00:35: Build scoreTrackII...
INFO @ Fri, 14 Apr 2017 00:01:54: Values in your input bedGraph files will be multiplied by 92.229774 ...
INFO @ Fri, 14 Apr 2017 00:12:27: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Fri, 14 Apr 2017 00:15:25: Write bedGraph of scores...
INFO @ Fri, 14 Apr 2017 00:21:23: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_ppois.bdg'!
|
Num | 10 | ID | task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_19 | Name | macs2 n/s rep2-pr1 | Thread | thread_Root | PID | 47046 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 22:52:07 | End | 2017-04-13 23:09:56 | Elapsed | 00:17:49 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
23460 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 22:52:31:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 22:52:31: #1 read tag files...
INFO @ Thu, 13 Apr 2017 22:52:31: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 22:52:32: 1000000
INFO @ Thu, 13 Apr 2017 22:52:34: 2000000
INFO @ Thu, 13 Apr 2017 22:52:35: 3000000
INFO @ Thu, 13 Apr 2017 22:52:37: 4000000
INFO @ Thu, 13 Apr 2017 22:52:38: 5000000
INFO @ Thu, 13 Apr 2017 22:52:40: 6000000
INFO @ Thu, 13 Apr 2017 22:52:41: 7000000
INFO @ Thu, 13 Apr 2017 22:52:43: 8000000
INFO @ Thu, 13 Apr 2017 22:52:44: 9000000
INFO @ Thu, 13 Apr 2017 22:52:46: 10000000
INFO @ Thu, 13 Apr 2017 22:52:47: 11000000
INFO @ Thu, 13 Apr 2017 22:52:49: 12000000
INFO @ Thu, 13 Apr 2017 22:52:50: 13000000
INFO @ Thu, 13 Apr 2017 22:52:52: 14000000
INFO @ Thu, 13 Apr 2017 22:52:53: 15000000
INFO @ Thu, 13 Apr 2017 22:52:55: 16000000
INFO @ Thu, 13 Apr 2017 22:52:56: 17000000
INFO @ Thu, 13 Apr 2017 22:52:58: 18000000
INFO @ Thu, 13 Apr 2017 22:52:59: 19000000
INFO @ Thu, 13 Apr 2017 22:53:01: 20000000
INFO @ Thu, 13 Apr 2017 22:53:02: 21000000
INFO @ Thu, 13 Apr 2017 22:53:04: 22000000
INFO @ Thu, 13 Apr 2017 22:53:05: 23000000
INFO @ Thu, 13 Apr 2017 22:53:07: 24000000
INFO @ Thu, 13 Apr 2017 22:53:08: 25000000
INFO @ Thu, 13 Apr 2017 22:53:10: 26000000
INFO @ Thu, 13 Apr 2017 22:53:11: 27000000
INFO @ Thu, 13 Apr 2017 22:53:12: 28000000
INFO @ Thu, 13 Apr 2017 22:53:14: 29000000
INFO @ Thu, 13 Apr 2017 22:53:15: 30000000
INFO @ Thu, 13 Apr 2017 22:53:17: 31000000
INFO @ Thu, 13 Apr 2017 22:53:18: 32000000
INFO @ Thu, 13 Apr 2017 22:53:20: 33000000
INFO @ Thu, 13 Apr 2017 22:53:21: 34000000
INFO @ Thu, 13 Apr 2017 22:53:23: 35000000
INFO @ Thu, 13 Apr 2017 22:53:24: 36000000
INFO @ Thu, 13 Apr 2017 22:53:26: 37000000
INFO @ Thu, 13 Apr 2017 22:53:27: 38000000
INFO @ Thu, 13 Apr 2017 22:53:29: 39000000
INFO @ Thu, 13 Apr 2017 22:53:30: 40000000
INFO @ Thu, 13 Apr 2017 22:53:32: 41000000
INFO @ Thu, 13 Apr 2017 22:53:33: 42000000
INFO @ Thu, 13 Apr 2017 22:53:35: 43000000
INFO @ Thu, 13 Apr 2017 22:53:36: 44000000
INFO @ Thu, 13 Apr 2017 22:53:38: 45000000
INFO @ Thu, 13 Apr 2017 22:53:39: 46000000
INFO @ Thu, 13 Apr 2017 22:53:42: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 22:53:44: 1000000
INFO @ Thu, 13 Apr 2017 22:53:45: 2000000
INFO @ Thu, 13 Apr 2017 22:53:47: 3000000
INFO @ Thu, 13 Apr 2017 22:53:48: 4000000
INFO @ Thu, 13 Apr 2017 22:53:50: 5000000
INFO @ Thu, 13 Apr 2017 22:53:52: 6000000
INFO @ Thu, 13 Apr 2017 22:53:53: 7000000
INFO @ Thu, 13 Apr 2017 22:53:54: 8000000
INFO @ Thu, 13 Apr 2017 22:53:56: 9000000
INFO @ Thu, 13 Apr 2017 22:53:57: 10000000
INFO @ Thu, 13 Apr 2017 22:53:59: 11000000
INFO @ Thu, 13 Apr 2017 22:54:00: 12000000
INFO @ Thu, 13 Apr 2017 22:54:02: 13000000
INFO @ Thu, 13 Apr 2017 22:54:03: 14000000
INFO @ Thu, 13 Apr 2017 22:54:05: 15000000
INFO @ Thu, 13 Apr 2017 22:54:06: 16000000
INFO @ Thu, 13 Apr 2017 22:54:08: 17000000
INFO @ Thu, 13 Apr 2017 22:54:09: 18000000
INFO @ Thu, 13 Apr 2017 22:54:11: 19000000
INFO @ Thu, 13 Apr 2017 22:54:12: 20000000
INFO @ Thu, 13 Apr 2017 22:54:14: 21000000
INFO @ Thu, 13 Apr 2017 22:54:15: 22000000
INFO @ Thu, 13 Apr 2017 22:54:17: 23000000
INFO @ Thu, 13 Apr 2017 22:54:18: 24000000
INFO @ Thu, 13 Apr 2017 22:54:20: 25000000
INFO @ Thu, 13 Apr 2017 22:54:21: 26000000
INFO @ Thu, 13 Apr 2017 22:54:23: 27000000
INFO @ Thu, 13 Apr 2017 22:54:24: 28000000
INFO @ Thu, 13 Apr 2017 22:54:26: 29000000
INFO @ Thu, 13 Apr 2017 22:54:27: 30000000
INFO @ Thu, 13 Apr 2017 22:54:28: 31000000
INFO @ Thu, 13 Apr 2017 22:54:30: 32000000
INFO @ Thu, 13 Apr 2017 22:54:31: 33000000
INFO @ Thu, 13 Apr 2017 22:54:33: 34000000
INFO @ Thu, 13 Apr 2017 22:54:34: 35000000
INFO @ Thu, 13 Apr 2017 22:54:36: 36000000
INFO @ Thu, 13 Apr 2017 22:54:37: 37000000
INFO @ Thu, 13 Apr 2017 22:54:39: 38000000
INFO @ Thu, 13 Apr 2017 22:54:40: 39000000
INFO @ Thu, 13 Apr 2017 22:54:42: 40000000
INFO @ Thu, 13 Apr 2017 22:54:43: 41000000
INFO @ Thu, 13 Apr 2017 22:54:45: 42000000
INFO @ Thu, 13 Apr 2017 22:54:46: 43000000
INFO @ Thu, 13 Apr 2017 22:54:48: 44000000
INFO @ Thu, 13 Apr 2017 22:54:49: 45000000
INFO @ Thu, 13 Apr 2017 22:54:51: 46000000
INFO @ Thu, 13 Apr 2017 22:54:52: 47000000
INFO @ Thu, 13 Apr 2017 22:54:54: 48000000
INFO @ Thu, 13 Apr 2017 22:54:55: 49000000
INFO @ Thu, 13 Apr 2017 22:54:57: 50000000
INFO @ Thu, 13 Apr 2017 22:54:58: 51000000
INFO @ Thu, 13 Apr 2017 22:55:00: 52000000
INFO @ Thu, 13 Apr 2017 22:55:01: 53000000
INFO @ Thu, 13 Apr 2017 22:55:03: 54000000
INFO @ Thu, 13 Apr 2017 22:55:04: 55000000
INFO @ Thu, 13 Apr 2017 22:55:06: 56000000
INFO @ Thu, 13 Apr 2017 22:55:07: 57000000
INFO @ Thu, 13 Apr 2017 22:55:08: 58000000
INFO @ Thu, 13 Apr 2017 22:55:10: 59000000
INFO @ Thu, 13 Apr 2017 22:55:11: 60000000
INFO @ Thu, 13 Apr 2017 22:55:13: 61000000
INFO @ Thu, 13 Apr 2017 22:55:14: 62000000
INFO @ Thu, 13 Apr 2017 22:55:16: 63000000
INFO @ Thu, 13 Apr 2017 22:55:17: 64000000
INFO @ Thu, 13 Apr 2017 22:55:19: 65000000
INFO @ Thu, 13 Apr 2017 22:55:20: 66000000
INFO @ Thu, 13 Apr 2017 22:55:22: 67000000
INFO @ Thu, 13 Apr 2017 22:55:23: 68000000
INFO @ Thu, 13 Apr 2017 22:55:25: 69000000
INFO @ Thu, 13 Apr 2017 22:55:26: 70000000
INFO @ Thu, 13 Apr 2017 22:55:28: 71000000
INFO @ Thu, 13 Apr 2017 22:55:29: 72000000
INFO @ Thu, 13 Apr 2017 22:55:31: 73000000
INFO @ Thu, 13 Apr 2017 22:55:32: 74000000
INFO @ Thu, 13 Apr 2017 22:55:34: 75000000
INFO @ Thu, 13 Apr 2017 22:55:35: 76000000
INFO @ Thu, 13 Apr 2017 22:55:37: 77000000
INFO @ Thu, 13 Apr 2017 22:55:38: 78000000
INFO @ Thu, 13 Apr 2017 22:55:40: 79000000
INFO @ Thu, 13 Apr 2017 22:55:41: 80000000
INFO @ Thu, 13 Apr 2017 22:55:43: 81000000
INFO @ Thu, 13 Apr 2017 22:55:44: 82000000
INFO @ Thu, 13 Apr 2017 22:55:46: 83000000
INFO @ Thu, 13 Apr 2017 22:55:47: 84000000
INFO @ Thu, 13 Apr 2017 22:55:49: 85000000
INFO @ Thu, 13 Apr 2017 22:55:50: 86000000
INFO @ Thu, 13 Apr 2017 22:55:51: 87000000
INFO @ Thu, 13 Apr 2017 22:55:53: 88000000
INFO @ Thu, 13 Apr 2017 22:55:54: 89000000
INFO @ Thu, 13 Apr 2017 22:55:56: 90000000
INFO @ Thu, 13 Apr 2017 22:55:57: 91000000
INFO @ Thu, 13 Apr 2017 22:55:59: 92000000
INFO @ Thu, 13 Apr 2017 22:56:00: 93000000
INFO @ Thu, 13 Apr 2017 22:56:02: 94000000
INFO @ Thu, 13 Apr 2017 22:56:03: 95000000
INFO @ Thu, 13 Apr 2017 22:56:05: 96000000
INFO @ Thu, 13 Apr 2017 22:56:06: 97000000
INFO @ Thu, 13 Apr 2017 22:56:08: 98000000
INFO @ Thu, 13 Apr 2017 22:56:09: 99000000
INFO @ Thu, 13 Apr 2017 22:56:18: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 22:56:18: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 22:56:18: #1 total tags in treatment: 46114888
INFO @ Thu, 13 Apr 2017 22:56:18: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 22:56:18: #1 finished!
INFO @ Thu, 13 Apr 2017 22:56:18: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 22:56:18: #2 Skipped...
INFO @ Thu, 13 Apr 2017 22:56:18: #2 Use 240 as fragment length
INFO @ Thu, 13 Apr 2017 22:56:18: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 22:56:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 22:56:18: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 23:01:35: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 23:01:35: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 23:01:35: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 23:01:35: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 23:01:35: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 23:09:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 23:09:54: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 23:09:54: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 23:09:54: Done!
|
Num | 11 | ID | task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_20 | Name | macs2 n/s rep2-pr2 | Thread | thread_Root | PID | 47047 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-13 23:05:36 | End | 2017-04-13 23:32:56 | Elapsed | 00:27:20 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Dependencies | | |
# SYS command. line 68
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 69
export LC_COLLATE=C
# SYS command. line 74
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR
# SYS command. line 77
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
# SYS command. line 80
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_summits.bed
# SYS command. line 84
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 94
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -m FE
# SYS command. line 97
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph
# SYS command. line 98
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_FE.bdg
# SYS command. line 101
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 102
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bw
# SYS command. line 103
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 109
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 111
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 113
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 116
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph
# SYS command. line 117
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_ppois.bdg
# SYS command. line 120
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 121
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bw
# SYS command. line 122
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 124
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign"_control_lambda.bdg
# SYS command. line 126
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
42461 (process ID) old priority 0, new priority 19
--------------------Stderr--------------------
INFO @ Thu, 13 Apr 2017 23:06:01:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz']
# 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: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Thu, 13 Apr 2017 23:06:01: #1 read tag files...
INFO @ Thu, 13 Apr 2017 23:06:01: #1 read treatment tags...
INFO @ Thu, 13 Apr 2017 23:06:04: 1000000
INFO @ Thu, 13 Apr 2017 23:06:05: 2000000
INFO @ Thu, 13 Apr 2017 23:06:07: 3000000
INFO @ Thu, 13 Apr 2017 23:06:09: 4000000
INFO @ Thu, 13 Apr 2017 23:06:11: 5000000
INFO @ Thu, 13 Apr 2017 23:06:13: 6000000
INFO @ Thu, 13 Apr 2017 23:06:15: 7000000
INFO @ Thu, 13 Apr 2017 23:06:17: 8000000
INFO @ Thu, 13 Apr 2017 23:06:19: 9000000
INFO @ Thu, 13 Apr 2017 23:06:21: 10000000
INFO @ Thu, 13 Apr 2017 23:06:23: 11000000
INFO @ Thu, 13 Apr 2017 23:06:25: 12000000
INFO @ Thu, 13 Apr 2017 23:06:27: 13000000
INFO @ Thu, 13 Apr 2017 23:06:29: 14000000
INFO @ Thu, 13 Apr 2017 23:06:31: 15000000
INFO @ Thu, 13 Apr 2017 23:06:33: 16000000
INFO @ Thu, 13 Apr 2017 23:06:35: 17000000
INFO @ Thu, 13 Apr 2017 23:06:37: 18000000
INFO @ Thu, 13 Apr 2017 23:06:39: 19000000
INFO @ Thu, 13 Apr 2017 23:06:41: 20000000
INFO @ Thu, 13 Apr 2017 23:06:43: 21000000
INFO @ Thu, 13 Apr 2017 23:06:45: 22000000
INFO @ Thu, 13 Apr 2017 23:06:47: 23000000
INFO @ Thu, 13 Apr 2017 23:06:48: 24000000
INFO @ Thu, 13 Apr 2017 23:06:51: 25000000
INFO @ Thu, 13 Apr 2017 23:06:53: 26000000
INFO @ Thu, 13 Apr 2017 23:06:54: 27000000
INFO @ Thu, 13 Apr 2017 23:06:56: 28000000
INFO @ Thu, 13 Apr 2017 23:06:58: 29000000
INFO @ Thu, 13 Apr 2017 23:07:00: 30000000
INFO @ Thu, 13 Apr 2017 23:07:02: 31000000
INFO @ Thu, 13 Apr 2017 23:07:04: 32000000
INFO @ Thu, 13 Apr 2017 23:07:06: 33000000
INFO @ Thu, 13 Apr 2017 23:07:08: 34000000
INFO @ Thu, 13 Apr 2017 23:07:10: 35000000
INFO @ Thu, 13 Apr 2017 23:07:12: 36000000
INFO @ Thu, 13 Apr 2017 23:07:14: 37000000
INFO @ Thu, 13 Apr 2017 23:07:16: 38000000
INFO @ Thu, 13 Apr 2017 23:07:18: 39000000
INFO @ Thu, 13 Apr 2017 23:07:20: 40000000
INFO @ Thu, 13 Apr 2017 23:07:22: 41000000
INFO @ Thu, 13 Apr 2017 23:07:24: 42000000
INFO @ Thu, 13 Apr 2017 23:07:26: 43000000
INFO @ Thu, 13 Apr 2017 23:07:28: 44000000
INFO @ Thu, 13 Apr 2017 23:07:30: 45000000
INFO @ Thu, 13 Apr 2017 23:07:32: 46000000
INFO @ Thu, 13 Apr 2017 23:07:36: #1.2 read input tags...
INFO @ Thu, 13 Apr 2017 23:07:38: 1000000
INFO @ Thu, 13 Apr 2017 23:07:40: 2000000
INFO @ Thu, 13 Apr 2017 23:07:42: 3000000
INFO @ Thu, 13 Apr 2017 23:07:44: 4000000
INFO @ Thu, 13 Apr 2017 23:07:46: 5000000
INFO @ Thu, 13 Apr 2017 23:07:48: 6000000
INFO @ Thu, 13 Apr 2017 23:07:50: 7000000
INFO @ Thu, 13 Apr 2017 23:07:52: 8000000
INFO @ Thu, 13 Apr 2017 23:07:54: 9000000
INFO @ Thu, 13 Apr 2017 23:07:56: 10000000
INFO @ Thu, 13 Apr 2017 23:07:58: 11000000
INFO @ Thu, 13 Apr 2017 23:08:00: 12000000
INFO @ Thu, 13 Apr 2017 23:08:02: 13000000
INFO @ Thu, 13 Apr 2017 23:08:04: 14000000
INFO @ Thu, 13 Apr 2017 23:08:06: 15000000
INFO @ Thu, 13 Apr 2017 23:08:08: 16000000
INFO @ Thu, 13 Apr 2017 23:08:10: 17000000
INFO @ Thu, 13 Apr 2017 23:08:12: 18000000
INFO @ Thu, 13 Apr 2017 23:08:14: 19000000
INFO @ Thu, 13 Apr 2017 23:08:16: 20000000
INFO @ Thu, 13 Apr 2017 23:08:18: 21000000
INFO @ Thu, 13 Apr 2017 23:08:20: 22000000
INFO @ Thu, 13 Apr 2017 23:08:22: 23000000
INFO @ Thu, 13 Apr 2017 23:08:24: 24000000
INFO @ Thu, 13 Apr 2017 23:08:26: 25000000
INFO @ Thu, 13 Apr 2017 23:08:28: 26000000
INFO @ Thu, 13 Apr 2017 23:08:30: 27000000
INFO @ Thu, 13 Apr 2017 23:08:32: 28000000
INFO @ Thu, 13 Apr 2017 23:08:34: 29000000
INFO @ Thu, 13 Apr 2017 23:08:36: 30000000
INFO @ Thu, 13 Apr 2017 23:08:38: 31000000
INFO @ Thu, 13 Apr 2017 23:08:40: 32000000
INFO @ Thu, 13 Apr 2017 23:08:42: 33000000
INFO @ Thu, 13 Apr 2017 23:08:44: 34000000
INFO @ Thu, 13 Apr 2017 23:08:46: 35000000
INFO @ Thu, 13 Apr 2017 23:08:48: 36000000
INFO @ Thu, 13 Apr 2017 23:08:50: 37000000
INFO @ Thu, 13 Apr 2017 23:08:52: 38000000
INFO @ Thu, 13 Apr 2017 23:08:54: 39000000
INFO @ Thu, 13 Apr 2017 23:08:55: 40000000
INFO @ Thu, 13 Apr 2017 23:08:57: 41000000
INFO @ Thu, 13 Apr 2017 23:08:59: 42000000
INFO @ Thu, 13 Apr 2017 23:09:01: 43000000
INFO @ Thu, 13 Apr 2017 23:09:03: 44000000
INFO @ Thu, 13 Apr 2017 23:09:05: 45000000
INFO @ Thu, 13 Apr 2017 23:09:07: 46000000
INFO @ Thu, 13 Apr 2017 23:09:09: 47000000
INFO @ Thu, 13 Apr 2017 23:09:11: 48000000
INFO @ Thu, 13 Apr 2017 23:09:13: 49000000
INFO @ Thu, 13 Apr 2017 23:09:15: 50000000
INFO @ Thu, 13 Apr 2017 23:09:17: 51000000
INFO @ Thu, 13 Apr 2017 23:09:19: 52000000
INFO @ Thu, 13 Apr 2017 23:09:21: 53000000
INFO @ Thu, 13 Apr 2017 23:09:23: 54000000
INFO @ Thu, 13 Apr 2017 23:09:25: 55000000
INFO @ Thu, 13 Apr 2017 23:09:27: 56000000
INFO @ Thu, 13 Apr 2017 23:09:29: 57000000
INFO @ Thu, 13 Apr 2017 23:09:31: 58000000
INFO @ Thu, 13 Apr 2017 23:09:33: 59000000
INFO @ Thu, 13 Apr 2017 23:09:35: 60000000
INFO @ Thu, 13 Apr 2017 23:09:37: 61000000
INFO @ Thu, 13 Apr 2017 23:09:39: 62000000
INFO @ Thu, 13 Apr 2017 23:09:42: 63000000
INFO @ Thu, 13 Apr 2017 23:09:44: 64000000
INFO @ Thu, 13 Apr 2017 23:09:45: 65000000
INFO @ Thu, 13 Apr 2017 23:09:47: 66000000
INFO @ Thu, 13 Apr 2017 23:09:49: 67000000
INFO @ Thu, 13 Apr 2017 23:09:51: 68000000
INFO @ Thu, 13 Apr 2017 23:09:53: 69000000
INFO @ Thu, 13 Apr 2017 23:09:55: 70000000
INFO @ Thu, 13 Apr 2017 23:09:57: 71000000
INFO @ Thu, 13 Apr 2017 23:09:59: 72000000
INFO @ Thu, 13 Apr 2017 23:10:01: 73000000
INFO @ Thu, 13 Apr 2017 23:10:03: 74000000
INFO @ Thu, 13 Apr 2017 23:10:05: 75000000
INFO @ Thu, 13 Apr 2017 23:10:07: 76000000
INFO @ Thu, 13 Apr 2017 23:10:09: 77000000
INFO @ Thu, 13 Apr 2017 23:10:11: 78000000
INFO @ Thu, 13 Apr 2017 23:10:13: 79000000
INFO @ Thu, 13 Apr 2017 23:10:15: 80000000
INFO @ Thu, 13 Apr 2017 23:10:17: 81000000
INFO @ Thu, 13 Apr 2017 23:10:18: 82000000
INFO @ Thu, 13 Apr 2017 23:10:20: 83000000
INFO @ Thu, 13 Apr 2017 23:10:22: 84000000
INFO @ Thu, 13 Apr 2017 23:10:24: 85000000
INFO @ Thu, 13 Apr 2017 23:10:26: 86000000
INFO @ Thu, 13 Apr 2017 23:10:28: 87000000
INFO @ Thu, 13 Apr 2017 23:10:30: 88000000
INFO @ Thu, 13 Apr 2017 23:10:32: 89000000
INFO @ Thu, 13 Apr 2017 23:10:34: 90000000
INFO @ Thu, 13 Apr 2017 23:10:36: 91000000
INFO @ Thu, 13 Apr 2017 23:10:38: 92000000
INFO @ Thu, 13 Apr 2017 23:10:40: 93000000
INFO @ Thu, 13 Apr 2017 23:10:42: 94000000
INFO @ Thu, 13 Apr 2017 23:10:44: 95000000
INFO @ Thu, 13 Apr 2017 23:10:46: 96000000
INFO @ Thu, 13 Apr 2017 23:10:47: 97000000
INFO @ Thu, 13 Apr 2017 23:10:49: 98000000
INFO @ Thu, 13 Apr 2017 23:10:51: 99000000
INFO @ Thu, 13 Apr 2017 23:11:02: #1 tag size is determined as 101 bps
INFO @ Thu, 13 Apr 2017 23:11:02: #1 tag size = 101
INFO @ Thu, 13 Apr 2017 23:11:02: #1 total tags in treatment: 46114886
INFO @ Thu, 13 Apr 2017 23:11:02: #1 total tags in control: 99976272
INFO @ Thu, 13 Apr 2017 23:11:02: #1 finished!
INFO @ Thu, 13 Apr 2017 23:11:02: #2 Build Peak Model...
INFO @ Thu, 13 Apr 2017 23:11:02: #2 Skipped...
INFO @ Thu, 13 Apr 2017 23:11:02: #2 Use 240 as fragment length
INFO @ Thu, 13 Apr 2017 23:11:02: #3 Call peaks...
INFO @ Thu, 13 Apr 2017 23:11:02: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Thu, 13 Apr 2017 23:11:02: #3 Pre-compute pvalue-qvalue table...
INFO @ Thu, 13 Apr 2017 23:20:28: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Thu, 13 Apr 2017 23:20:28: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_treat_pileup.bdg
INFO @ Thu, 13 Apr 2017 23:20:28: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_control_lambda.bdg
INFO @ Thu, 13 Apr 2017 23:20:28: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Thu, 13 Apr 2017 23:20:28: #3 Call peaks for each chromosome...
INFO @ Thu, 13 Apr 2017 23:32:51: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.xls
INFO @ Thu, 13 Apr 2017 23:32:52: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_peaks.narrowPeak
INFO @ Thu, 13 Apr 2017 23:32:52: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign_summits.bed
INFO @ Thu, 13 Apr 2017 23:32:53: Done!
|
Num | 12 | ID | task.callpeak_naive_overlap.naive_overlap.line_143.id_21 | Name | naive_overlap | Thread | thread_Root | PID | 47048 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 01:55:28 | End | 2017-04-14 01:56:45 | Elapsed | 00:01:17 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 145
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 148
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.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 <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.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 -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.PooledInReps.narrowPeak.gz
# SYS command. line 151
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.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 <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.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 -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz
# SYS command. line 154
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.narrowPeak.gz
# SYS command. line 156
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.gz
# SYS command. line 158
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz
# SYS command. line 160
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
22599 (process ID) old priority 0, new priority 19
Waiting for 58 seconds.
|
Num | 13 | ID | task.callpeak_idr.idr2_rep1_rep2.line_74.id_22 | Name | idr2 rep1-rep2 | Thread | thread_Root | PID | 47049 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 01:56:47 | End | 2017-04-14 01:59:37 | Elapsed | 00:02:50 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
| Dependencies | | |
# SYS command. line 76
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 78
idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.log.txt
# SYS command. line 82
idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 85
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz
# SYS command. line 88
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.narrowPeak.gz
# SYS command. line 89
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.12-col.bed.gz
# SYS command. line 91
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz
# SYS command. line 92
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
# SYS command. line 93
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
# SYS command. line 95
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt
# SYS command. line 96
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz
# SYS command. line 98
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
25411 (process ID) old priority 0, new priority 19
|
Num | 14 | ID | task.callpeak_idr.idr2_rep1_pr.line_74.id_23 | Name | idr2 rep1-pr | Thread | thread_Root | PID | 47050 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 01:56:48 | End | 2017-04-14 02:03:34 | Elapsed | 00:06:46 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
| Dependencies | | |
# SYS command. line 76
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 78
idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.log.txt
# SYS command. line 82
idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 85
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz
# SYS command. line 88
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.narrowPeak.gz
# SYS command. line 89
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.12-col.bed.gz
# SYS command. line 91
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 92
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
# SYS command. line 93
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
# SYS command. line 95
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt
# SYS command. line 96
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 98
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
43321 (process ID) old priority 0, new priority 19
|
Num | 15 | ID | task.callpeak_idr.idr2_rep2_pr.line_74.id_24 | Name | idr2 rep2-pr | Thread | thread_Root | PID | 47051 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 01:56:49 | End | 2017-04-14 02:00:46 | Elapsed | 00:03:57 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
| Dependencies | | |
# SYS command. line 76
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 78
idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.log.txt
# SYS command. line 82
idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 85
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz
# SYS command. line 88
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.narrowPeak.gz
# SYS command. line 89
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.12-col.bed.gz
# SYS command. line 91
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 92
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
# SYS command. line 93
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
# SYS command. line 95
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt
# SYS command. line 96
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 98
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
25412 (process ID) old priority 0, new priority 19
|
Num | 16 | ID | task.callpeak_idr.idr2_ppr.line_74.id_25 | Name | idr2 ppr | Thread | thread_Root | PID | 47052 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 01:56:50 | End | 2017-04-14 01:59:30 | Elapsed | 00:02:40 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
| Dependencies | | |
# SYS command. line 76
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 78
idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.log.txt
# SYS command. line 82
idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 85
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz
# SYS command. line 88
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.narrowPeak.gz
# SYS command. line 89
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.12-col.bed.gz
# SYS command. line 91
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 92
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
# SYS command. line 93
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
# SYS command. line 95
gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt
# SYS command. line 96
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz
# SYS command. line 98
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
43322 (process ID) old priority 0, new priority 19
|
Num | 17 | ID | task.sys.copy_file.line_131.id_34 | Name | copy file | Thread | thread_Root | PID | 45503 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:35 | End | 2017-04-14 02:03:36 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 133
cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
# SYS command. line 134
while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
|
Num | 18 | ID | task.sys.copy_file.line_131.id_35 | Name | copy file | Thread | thread_Root | PID | 45508 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:35 | End | 2017-04-14 02:03:36 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 133
cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
# SYS command. line 134
while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
|
Num | 19 | ID | task.sys.copy_file.line_131.id_36 | Name | copy file | Thread | thread_Root | PID | 45513 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:35 | End | 2017-04-14 02:03:36 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
| Dependencies | | |
# SYS command. line 133
cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
# SYS command. line 134
while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
|
Num | 20 | ID | task.sys.copy_file.line_131.id_37 | Name | copy file | Thread | thread_Root | PID | 45530 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:36 | End | 2017-04-14 02:03:36 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
| Dependencies | | |
# SYS command. line 133
cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
# SYS command. line 134
while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
|
Num | 21 | ID | task.callpeak_idr.idr_final_qc.line_283.id_38 | Name | idr final qc | Thread | thread_Root | PID | 47053 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:37 | End | 2017-04-14 02:05:00 | Elapsed | 00:01:23 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/ZBTB26_MACS2_IDR_final.qc
| Dependencies | | |
# SYS command. line 285
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 287
echo -e "Nt\tN1 N2 ""Np\tN_opt\tN_consv\topt_set\tconsv_set\trescue_ratio\tself_consistency_ratio\treproducibility_test" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/ZBTB26_MACS2_IDR_final.qc
# SYS command. line 288
echo -e "15282\t14000 14479 ""14767\t15282\t15282\trep1-rep2\trep1-rep2\t1.0348750592537415\t1.0342142857142858\tpass" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/ZBTB26_MACS2_IDR_final.qc
# SYS command. line 290
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
45503 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.
|
Num | 22 | ID | task.callpeak_idr.FRiP_rep1_pr.line_120.id_39 | Name | FRiP rep1-pr | Thread | thread_Root | PID | 47054 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:38 | End | 2017-04-14 02:09:01 | Elapsed | 00:05:22 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc
| Dependencies | | |
# SYS command. line 121
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 123
val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -118 -r 118 | \
awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)
# SYS command. line 133
val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz | wc -l)
# SYS command. line 134
awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc
# SYS command. line 135
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
46132 (process ID) old priority 0, new priority 19
|
Num | 23 | ID | task.callpeak_idr.FRiP_rep2_pr.line_120.id_40 | Name | FRiP rep2-pr | Thread | thread_Root | PID | 47055 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:40 | End | 2017-04-14 02:08:13 | Elapsed | 00:04:33 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc
| Dependencies | | |
# SYS command. line 121
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 123
val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -120 -r 120 | \
awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)
# SYS command. line 133
val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz | wc -l)
# SYS command. line 134
awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc
# SYS command. line 135
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
45505 (process ID) old priority 0, new priority 19
|
Num | 24 | ID | task.callpeak_idr.FRiP_ppr.line_120.id_41 | Name | FRiP ppr | Thread | thread_Root | PID | 47056 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:41 | End | 2017-04-14 02:12:36 | Elapsed | 00:08:54 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc
| Dependencies | | |
# SYS command. line 121
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 123
val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -119 -r 119 | \
awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)
# SYS command. line 133
val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz | wc -l)
# SYS command. line 134
awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc
# SYS command. line 135
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
46127 (process ID) old priority 0, new priority 19
|
Num | 25 | ID | task.callpeak_idr.FRiP_rep1_rep2.line_120.id_42 | Name | FRiP rep1-rep2 | Thread | thread_Root | PID | 47057 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:03:43 | End | 2017-04-14 02:14:36 | Elapsed | 00:10:53 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc
| Dependencies | | |
# SYS command. line 121
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 123
val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -119 -r 119 | \
awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)
# SYS command. line 133
val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz | wc -l)
# SYS command. line 134
awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc
# SYS command. line 135
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
45502 (process ID) old priority 0, new priority 19
|
Num | 26 | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_43 | Name | blacklist_filter peak_pooled | Thread | thread_Root | PID | 23854 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:14:38 | End | 2017-04-14 02:15:46 | Elapsed | 00:01:07 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 29
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 31
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) \
| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
23858 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.
|
Num | 27 | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_44 | Name | blacklist_filter peak 1 | Thread | thread_Root | PID | 23874 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:14:39 | End | 2017-04-14 02:15:47 | Elapsed | 00:01:07 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 29
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 31
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) \
| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
23879 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.
|
Num | 28 | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_45 | Name | blacklist_filter peak 2 | Thread | thread_Root | PID | 23940 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:14:40 | End | 2017-04-14 02:15:48 | Elapsed | 00:01:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 29
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 31
bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) \
| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
23945 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.
|
Num | 29 | ID | task.report.peak2hammock.line_361.id_48 | Name | peak2hammock | Thread | thread_Root | PID | 26712 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:15:49 | End | 2017-04-14 02:15:58 | Elapsed | 00:00:09 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
| Dependencies | | |
# SYS command. line 363
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 364
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.tmp
# SYS command. line 366
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.hammock
# SYS command. line 367
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_4000_GRCh38.PE2SE.tagAlign.naive_overlap.filt.narrowPeak.tmp
--------------------Stdout--------------------
26721 (process ID) old priority 0, new priority 19
|
Num | 30 | ID | task.report.peak2hammock.line_361.id_49 | Name | peak2hammock | Thread | thread_Root | PID | 27115 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:15:59 | End | 2017-04-14 02:16:08 | Elapsed | 00:00:09 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock.gz
| Dependencies | | |
# SYS command. line 363
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 364
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp
# SYS command. line 366
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock
# SYS command. line 367
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp
--------------------Stdout--------------------
27121 (process ID) old priority 0, new priority 19
|
Num | 31 | ID | task.report.peak2hammock.line_361.id_50 | Name | peak2hammock | Thread | thread_Root | PID | 27589 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:16:09 | End | 2017-04-14 02:16:18 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock.gz
| Dependencies | | |
# SYS command. line 363
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 364
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp
# SYS command. line 366
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock
# SYS command. line 367
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp
--------------------Stdout--------------------
27593 (process ID) old priority 0, new priority 19
|
Num | 32 | ID | task.report.peak2hammock.line_361.id_51 | Name | peak2hammock | Thread | thread_Root | PID | 28044 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:16:19 | End | 2017-04-14 02:16:28 | Elapsed | 00:00:09 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
| Dependencies | | |
# SYS command. line 363
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 364
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp
# SYS command. line 366
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock
# SYS command. line 367
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp
--------------------Stdout--------------------
28048 (process ID) old priority 0, new priority 19
|
Num | 33 | ID | task.report.peak2hammock.line_361.id_52 | Name | peak2hammock | Thread | thread_Root | PID | 28458 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:16:29 | End | 2017-04-14 02:16:38 | Elapsed | 00:00:09 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock.gz
| Dependencies | | |
# SYS command. line 363
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 364
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp
# SYS command. line 366
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock
# SYS command. line 367
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp
--------------------Stdout--------------------
28462 (process ID) old priority 0, new priority 19
|
Num | 34 | ID | task.graphviz.report.line_97.id_53 | Name | report | Thread | thread_Root | PID | 28893 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:16:39 | End | 2017-04-14 02:16:47 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | | Output files | | Dependencies | | |
# SYS command. line 98
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout--------------------
28897 (process ID) old priority 0, new priority 19
|
Num | 35 | ID | task.report.pdf2png.line_328.id_54 | Name | pdf2png | Thread | thread_Root | PID | 28955 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:16:39 | End | 2017-04-14 02:16:48 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.png
| Dependencies | | |
# SYS command. line 329
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 330
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf
--------------------Stdout--------------------
28961 (process ID) old priority 0, new priority 19
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Num | 36 | ID | task.report.pdf2png.line_328.id_55 | Name | pdf2png | Thread | thread_Root | PID | 28960 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-04-14 02:16:39 | End | 2017-04-14 02:16:48 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.png
| Dependencies | | |
# SYS command. line 329
if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi
# SYS command. line 330
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf
--------------------Stdout--------------------
28969 (process ID) old priority 0, new priority 19
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