BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170413_220547_667
Start time 2017-04-13 22:05:47
Run time 04:11:00.854
Tasks executed 36
Tasks failed 0
Tasks failed names
 
Arguments* [-title, ZBTB26_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz, -pe, -macs2_for_idr, $]
System* sge
Cpus* -1
Exit value 0
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None
 chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_12
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_13
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_14
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_15
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_16
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_17
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_18
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_19
chipseq.bds.20170413_220547_667/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_20
chipseq.bds.20170413_220547_667/task.callpeak_naive_overlap.naive_overlap.line_143.id_21
chipseq.bds.20170413_220547_667/task.callpeak_idr.idr2_rep1_rep2.line_74.id_22
chipseq.bds.20170413_220547_667/task.callpeak_idr.idr2_rep1_pr.line_74.id_23
chipseq.bds.20170413_220547_667/task.callpeak_idr.idr2_rep2_pr.line_74.id_24
chipseq.bds.20170413_220547_667/task.callpeak_idr.idr2_ppr.line_74.id_25
chipseq.bds.20170413_220547_667/task.sys.copy_file.line_131.id_34
chipseq.bds.20170413_220547_667/task.sys.copy_file.line_131.id_35
chipseq.bds.20170413_220547_667/task.sys.copy_file.line_131.id_36
chipseq.bds.20170413_220547_667/task.sys.copy_file.line_131.id_37
chipseq.bds.20170413_220547_667/task.callpeak_idr.idr_final_qc.line_283.id_38
chipseq.bds.20170413_220547_667/task.callpeak_idr.FRiP_rep1_pr.line_120.id_39
chipseq.bds.20170413_220547_667/task.callpeak_idr.FRiP_rep2_pr.line_120.id_40
chipseq.bds.20170413_220547_667/task.callpeak_idr.FRiP_ppr.line_120.id_41
chipseq.bds.20170413_220547_667/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_42
chipseq.bds.20170413_220547_667/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_43
chipseq.bds.20170413_220547_667/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_44
chipseq.bds.20170413_220547_667/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_45
chipseq.bds.20170413_220547_667/task.report.peak2hammock.line_361.id_48
chipseq.bds.20170413_220547_667/task.report.peak2hammock.line_361.id_49
chipseq.bds.20170413_220547_667/task.report.peak2hammock.line_361.id_50
chipseq.bds.20170413_220547_667/task.report.peak2hammock.line_361.id_51
chipseq.bds.20170413_220547_667/task.report.peak2hammock.line_361.id_52
chipseq.bds.20170413_220547_667/task.graphviz.report.line_97.id_53
chipseq.bds.20170413_220547_667/task.report.pdf2png.line_328.id_54
chipseq.bds.20170413_220547_667/task.report.pdf2png.line_328.id_55
 
thread_41 thread_Root
 chipseq.bds.20170413_220547_667_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_11
 
thread_43 thread_Root
  
thread_42 thread_Root
 chipseq.bds.20170413_220547_667_parallel_42/task.postalign_bed.xcor_rep2.line_212.id_10
 

Task details

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

  
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

  

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
string _LMFILES_ /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/ucsc_tools/3.0.9
bool allowEmpty false
string[] args [-title, ZBTB26_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_4000_GRCh38.PE2SE.tagAlign.gz, -pe, -macs2_for_idr, $]
bool canFail false
string CPATH /users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int cpus -1
int cpusLocal 56
int day 86400
string DEEPLIFT_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:11.0
real E 2.718281828459045
string ENHANCER_SCRIPTS_DIR /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
string EVENT_NOEPOLL 1
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KERAS_DIR /users/imk1/.local/lib/python2.7/site-packages/keras/
string KRB5CCNAME FILE:/tmp/krb5cc_1048_CCx82k
string LANG en_US.UTF-8
string LIBRARY_PATH /users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string LOADEDMODULES modsappsdir/modsappsdir:ucsc_tools/3.0.9
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string MODULESAPPSDIR /software
string MODULESHOME /software/env_module/3.2.10
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string node
int P 1125899906842624
string PATH /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts//exec:/users/imk1/edirect:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/software/ucsc_tools/3.0.9:/software/ucsc_tools/3.0.9/blat
string PERL5LIB /users/imk1/perl5/lib/perl5
string PERL_LOCAL_LIB_ROOT /users/imk1/perl5
string PERL_MB_OPT --install_base \"/users/imk1/perl5\"
string PERL_MM_OPT INSTALL_BASE=/users/imk1/perl5
real PI 3.141592653589793
string ppwd /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2
string programName chipseq.bds
string programPath /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string PWD /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2
string PYTHONPATH /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string queue
int retry 0
string RULEFITBASE /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string SHELL /bin/bash
string SHLVL 4
string SSH_CLIENT 171.65.77.8 57066 22
string SSH_CONNECTION 171.65.77.8 57066 171.65.76.63 22
string SSH_TTY /dev/pts/4
string STY 53311.ZBTB26_MACS2.BDS
string system sge
int T 1099511627776
string TERM screen
string TERMCAP SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int timeout -1
string TMUX /tmp/tmux-1048/default,43619,0
string TMUX_PANE %0
string USER imk1
string UTIL_SCRIPTS_DIR /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/
int walltimeout 8640000
int week 604800
string WINDOW 0
string XDG_RUNTIME_DIR /run/user/1048
string XDG_SESSION_ID 67062
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt