BigDataScript report: chipseq.bds

Script file /mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170905_182735_334
Start time 2017-09-05 18:27:35
Run time 13:00:33.333
Tasks executed 11
Tasks failed 1
Tasks failed names 
FRiP rep1-rep2
Arguments* [-out_dir, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF, -screen, test2, -no_browser_tracks, -true_rep, -type, TF, -species, hg19, -subsample_chip, 0, -se, -ctl_tag1, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.shuffle.tagAlign.gz, -ctl_tag2, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz, -tag1, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.tagAlign.gz, -tag2, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz, $]
System* sge
Cpus* -1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None 
 chipseq.bds.20170905_182735_334/task.callpeak_spp.spp_pooled_rep.line_68.id_18
chipseq.bds.20170905_182735_334/task.callpeak_spp.spp_rep1.line_68.id_19
chipseq.bds.20170905_182735_334/task.callpeak_spp.spp_rep2.line_68.id_20
chipseq.bds.20170905_182735_334/task.callpeak_naive_overlap.naive_overlap.line_143.id_21
chipseq.bds.20170905_182735_334/task.callpeak_idr.idr2_rep1_rep2.line_74.id_30
chipseq.bds.20170905_182735_334/task.sys.copy_file.line_131.id_33
chipseq.bds.20170905_182735_334/task.sys.copy_file.line_131.id_34
chipseq.bds.20170905_182735_334/task.sys.copy_file.line_131.id_35
chipseq.bds.20170905_182735_334/task.sys.copy_file.line_131.id_36
chipseq.bds.20170905_182735_334/task.callpeak_idr.idr_final_qc.line_283.id_37
chipseq.bds.20170905_182735_334/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_38
thread_42 thread_Root
thread_41 thread_Root
thread_44 thread_Root
thread_43 thread_Root

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.callpeak_spp.spp_pooled_rep.line_68.id_18
Name spp pooled_rep
Thread thread_Root
PID 114160
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-05 18:28:15
End 2017-09-06 07:19:27
Elapsed 12:51:11
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.pdf
Dependencies 
 
# SYS command. line 70

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/.:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/modules:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/utils:${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 73

 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 77

 Rscript  ${RUN_SPP} -c=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz -p=1 -i=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz \
			-npeak=300000 -odir=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep -speak=145 -savr -savp -rf -out=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore

# SYS command. line 81

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz

# SYS command. line 83

 rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz

# SYS command. line 85

 mv /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.pdf /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.pdf

# SYS command. line 88

 if [ $(zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz; fi

# SYS command. line 91

 if [ ! -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 93

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/pipeline_genome_data/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | grep -P 'chr[\dXY]+[ \t]' \
			| gzip -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 99

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; sleep 0; fi
 
   
--------------------Stdout--------------------
34060 (process ID) old priority 0, new priority 19
################
ChIP data: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz 
Control data: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep 
narrowPeak output file name: NA 
regionPeak output file name: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.pdf 
result filename: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz 
opened /tmp/114160.1.q/Rtmpz6gxsQ/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign85c665fbb9d7
done. read 62479888 fragments
ChIP data read length 75 
[1] TRUE
Reading Control tagAlign/BAM file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz 
opened /tmp/114160.1.q/Rtmpz6gxsQ/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign85c6195c0616
done. read 62479796 fragments
Control data read length 75 
Calculating peak characteristics
Minimum cross-correlation value 0.3718012 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.461437368352876 
Top 3 estimates for fragment length 145 
Window half size 325 
Phantom peak location 80 
Phantom peak Correlation 0.3817123 
Normalized Strand cross-correlation coefficient (NSC) 1.241086 
Relative Strand cross-correlation Coefficient (RSC) 9.044001 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 1.09761  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.9110701  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000005 
Detected 1755806 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
Num 2
ID task.callpeak_spp.spp_rep1.line_68.id_19
Name spp rep1
Thread thread_Root
PID 114161
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-05 18:28:17
End 2017-09-06 06:46:55
Elapsed 12:18:38
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.tagAlign.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.pdf
Dependencies 
 
# SYS command. line 70

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/.:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/modules:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/utils:${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 73

 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 77

 Rscript  ${RUN_SPP} -c=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.tagAlign.gz -p=1 -i=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz \
			-npeak=300000 -odir=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore

# SYS command. line 81

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz

# SYS command. line 83

 rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz

# SYS command. line 85

 mv /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign.pdf /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.pdf

# SYS command. line 88

 if [ $(zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz; fi

# SYS command. line 91

 if [ ! -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 93

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/pipeline_genome_data/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | grep -P 'chr[\dXY]+[ \t]' \
			| gzip -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 99

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; sleep 0; fi
 
   
--------------------Stdout--------------------
34061 (process ID) old priority 0, new priority 19
################
ChIP data: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.tagAlign.gz 
Control data: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign.pdf 
result filename: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.tagAlign.gz 
opened /tmp/114161.1.q/RtmpI80wsQ/GM_HiChIP_cohesin.r1.self_lig.tagAlign85c95452bb22
done. read 28471230 fragments
ChIP data read length 75 
[1] TRUE
Reading Control tagAlign/BAM file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz 
opened /tmp/114161.1.q/RtmpI80wsQ/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign85c96e5a3bdc
done. read 62479796 fragments
Control data read length 75 
Calculating peak characteristics
Minimum cross-correlation value 0.2474131 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.319485798549097 
Top 3 estimates for fragment length 145 
Window half size 335 
Phantom peak location 80 
Phantom peak Correlation 0.2563666 
Normalized Strand cross-correlation coefficient (NSC) 1.291305 
Relative Strand cross-correlation Coefficient (RSC) 8.049707 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 2.412845  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.4144484  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000003 
Detected 1386451 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
Num 3
ID task.callpeak_spp.spp_rep2.line_68.id_20
Name spp rep2
Thread thread_Root
PID 114162
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-05 18:28:19
End 2017-09-06 05:58:25
Elapsed 11:30:06
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.pdf
Dependencies 
 
# SYS command. line 70

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/.:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/modules:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/utils:${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 73

 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 77

 Rscript  ${RUN_SPP} -c=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz -p=1 -i=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz \
			-npeak=300000 -odir=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2 -speak=145 -savr -savp -rf -out=/mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore

# SYS command. line 81

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz

# SYS command. line 83

 rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz

# SYS command. line 85

 mv /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign.pdf /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.pdf

# SYS command. line 88

 if [ $(zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz; fi

# SYS command. line 91

 if [ ! -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 93

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a <(zcat -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/data/pipeline_genome_data/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | grep -P 'chr[\dXY]+[ \t]' \
			| gzip -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 99

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; sleep 0; fi
 
   
--------------------Stdout--------------------
34063 (process ID) old priority 0, new priority 19
################
ChIP data: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz 
Control data: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2 
narrowPeak output file name: NA 
regionPeak output file name: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_VS_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign.pdf 
result filename: /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz 
opened /tmp/114162.1.q/Rtmp9gNShQ/GM_HiChIP_cohesin.r2.self_lig.tagAlign85ca283325eb
done. read 34008658 fragments
ChIP data read length 75 
[1] TRUE
Reading Control tagAlign/BAM file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_ctl/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz 
opened /tmp/114162.1.q/Rtmp9gNShQ/GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign85ca6656ca8a
done. read 62479796 fragments
Control data read length 75 
Calculating peak characteristics
Minimum cross-correlation value 0.2743796 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.345225456073559 
Top 3 estimates for fragment length 145 
Window half size 315 
Phantom peak location 80 
Phantom peak Correlation 0.2810189 
Normalized Strand cross-correlation coefficient (NSC) 1.258204 
Relative Strand cross-correlation Coefficient (RSC) 10.67064 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 1.957179  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.5109394  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000015 
Detected 1603148 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
Num 4
ID task.callpeak_naive_overlap.naive_overlap.line_143.id_21
Name naive_overlap
Thread thread_Root
PID 114163
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-06 07:19:29
End 2017-09-06 07:21:28
Elapsed 00:01:58
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline /mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/overlap/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.naive_overlap.filt.regionPeak.gz
Dependencies 
 
# SYS command. line 145

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/.:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/modules:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/utils:${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 /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz) -b <(zcat -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.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 /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.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 > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/overlap/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.PooledInReps.regionPeak.gz

# SYS command. line 151

 echo

# SYS command. line 154

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/overlap/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.PooledInReps.regionPeak.gz  | sort | uniq | gzip -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/overlap/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.naive_overlap.regionPeak.gz

# SYS command. line 156

 bedtools intersect -v -a <(zcat -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/overlap/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.naive_overlap.regionPeak.gz) -b <(zcat -f /mnt/data/pipeline_genome_data/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/overlap/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.naive_overlap.filt.regionPeak.gz

# SYS command. line 158

 rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/overlap/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.PooledInReps.regionPeak.gz 

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; sleep 0; fi
 
   
--------------------Stdout--------------------
6455 (process ID) old priority 0, new priority 19

Waiting for 53 seconds.
Num 5
ID task.callpeak_idr.idr2_rep1_rep2.line_74.id_30
Name idr2 rep1-rep2
Thread thread_Root
PID 114164
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-06 07:21:31
End 2017-09-06 07:26:28
Elapsed 00:04:57
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.unthresholded-peaks.txt.png /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.log.txt /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.unthresholded-peaks.txt.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Dependencies 
 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/.:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/modules:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/utils:${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 /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep1/GM_HiChIP_cohesin.r1.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/rep2/GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz --peak-list /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign_x_GM_HiChIP_cohesin.r1.self_lig.shuffle_GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_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"}' /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_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 > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_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 > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/pipeline_genome_data/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_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 > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_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 > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.13-col.bed.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_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}]; sleep 0; fi
 
   
--------------------Stdout--------------------
6557 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
/software/miniconda3/envs/aquas_chipseq_py3/lib/python3.5/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
/software/miniconda3/envs/aquas_chipseq_py3/lib/python3.5/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
Num 6
ID task.sys.copy_file.line_131.id_33
Name copy file
Thread thread_Root
PID 35934
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-06 07:26:29
End 2017-09-06 07:26:29
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/optimal_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Dependencies 
 
# SYS command. line 133

 cp --remove-destination /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/optimal_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/optimal_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
Num 7
ID task.sys.copy_file.line_131.id_34
Name copy file
Thread thread_Root
PID 35940
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-06 07:26:29
End 2017-09-06 07:26:29
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/conservative_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Dependencies 
 
# SYS command. line 133

 cp --remove-destination /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/conservative_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/conservative_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
Num 8
ID task.sys.copy_file.line_131.id_35
Name copy file
Thread thread_Root
PID 35952
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-06 07:26:29
End 2017-09-06 07:26:29
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/optimal_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Dependencies 
 
# SYS command. line 133

 cp --remove-destination /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/optimal_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/optimal_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
Num 9
ID task.sys.copy_file.line_131.id_36
Name copy file
Thread thread_Root
PID 35963
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-06 07:26:29
End 2017-09-06 07:26:29
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/conservative_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz
Dependencies 
 
# SYS command. line 133

 cp --remove-destination /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/conservative_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/conservative_set/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
Num 10
ID task.callpeak_idr.idr_final_qc.line_283.id_37
Name idr final qc
Thread thread_Root
PID 114165
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2017-09-06 07:26:30
End 2017-09-06 07:28:08
Elapsed 00:01:37
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/qc/GM_HiChIP_cohesin_pipeline_TF_IDR_final.qc
Dependencies 
 
# SYS command. line 285

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/.:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/modules:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/utils:${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\t""Np\tN_opt\tN_consv\topt_set\tconsv_set\trescue_ratio\tself_consistency_ratio\treproducibility_test" > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/qc/GM_HiChIP_cohesin_pipeline_TF_IDR_final.qc

# SYS command. line 288

 echo -e "15902\t""0\t15902\t15902\trep1-rep2\trep1-rep2\t0.0\t1.0\tpass" >> /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/qc/GM_HiChIP_cohesin_pipeline_TF_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}]; sleep 0; fi
 
   
--------------------Stdout--------------------
6672 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.
Num 11
ID task.callpeak_idr.FRiP_rep1_rep2.line_120.id_38
Name FRiP rep1-rep2
Thread thread_Root
PID 114166
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-09-06 07:26:32
End 2017-09-06 07:26:32
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Output files /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc
Dependencies 
 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/.:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/modules:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/utils:${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 /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz -g /mnt/data/pipeline_genome_data/hg19/hg19.chrom.sizes -s -l -73 -r 73 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b <(zcat -f /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_rep1-rep2.IDR0.05.filt.narrowPeak.gz) -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/align/pooled_rep/GM_HiChIP_cohesin.r1.self_lig_GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF/peak/spp/idr/true_reps/rep1-rep2/GM_HiChIP_cohesin_pipeline_TF_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}]; sleep 0; fi
 
   
--------------------Stdout--------------------
6673 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Error: malformed BED entry at line 17694319. Start Coordinate detected that is < 0. Exiting.

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 114166
submission_time:            Wed Sep  6 07:26:32 2017
owner:                      oursu
uid:                        1029
group:                      users
gid:                        100
sge_o_home:                 /users/oursu/
sge_o_log_name:             oursu
sge_o_path:                 /srv/scratch/oursu/code/anaconda/anaconda/bin:/mnt/lab_data/kundaje/users/oursu/code/deeplearning//exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/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
sge_o_shell:                /bin/bash
sge_o_workdir:              /mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline
sge_o_host:                 nandi
account:                    sge
stderr_path_list:           NONE:NONE:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/chipseq.bds.20170905_182735_334/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_38.stderr.cluster
mail_list:                  oursu@nandi
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/chipseq.bds.20170905_182735_334/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_38.stdout.cluster
jobshare:                   0
env_list:                   MAIL=/var/mail/oursu,SSH_CLIENT=171.66.16.89 62920 22,USER=oursu,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=2,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/oursu/,SSH_TTY=/dev/pts/62,LOGNAME=oursu,_=/usr/bin/bds,XDG_SESSION_ID=47987,TERM=screen,DEEPLEARN_SCRIPTS_DIR=/mnt/lab_data/kundaje/users/oursu/code/deeplearning/,KERAS_DIR=/mnt/lab_data/kundaje/users/oursu/code/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/srv/scratch/oursu/code/anaconda/anaconda/bin:/mnt/lab_data/kundaje/users/oursu/code/deeplearning//exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,XDG_RUNTIME_DIR=/run/user/1029,DISPLAY=localhost:15.0,SGE_CELL=default,STY=28161.test2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,UTIL_SCRIPTS_DIR=/mnt/lab_data/kundaje/users/oursu/code/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.66.16.89 62920 171.65.76.244 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
scheduling info:            queue instance "q@kali" dropped because it is temporarily not available
                            queue instance "amd.q@amold" dropped because it is temporarily not available

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
bool allowEmpty false
string[] args [-out_dir, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin_pipeline_TF, -screen, test2, -no_browser_tracks, -true_rep, -type, TF, -species, hg19, -subsample_chip, 0, -se, -ctl_tag1, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.shuffle.tagAlign.gz, -ctl_tag2, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.shuffle.tagAlign.gz, -tag1, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r1.self_lig.tagAlign.gz, -tag2, /mnt/lab_data/kundaje/users/oursu/hichip/self_ligation/self_ligations_merged_techreps/dist1000/GM_HiChIP_cohesin.r2.self_lig.tagAlign.gz, $]
bool canFail false
int cpus -1
int cpusLocal 48
int day 86400
string DEEPLEARN_SCRIPTS_DIR /mnt/lab_data/kundaje/users/oursu/code/deeplearning/
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:15.0
real E 2.718281828459045
int G 1073741824
string HOME /users/oursu/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KERAS_DIR /mnt/lab_data/kundaje/users/oursu/code/keras/
string LANG en_US.UTF-8
string LOADEDMODULES
string LOGNAME oursu
int M 1048576
string MAIL /var/mail/oursu
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string MODULESHOME /software/env_module/3.2.10
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string node
int P 1125899906842624
string PATH /srv/scratch/oursu/code/anaconda/anaconda/bin:/mnt/lab_data/kundaje/users/oursu/code/deeplearning//exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/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
real PI 3.141592653589793
string ppwd /mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline
string programName chipseq.bds
string programPath /mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline/chipseq.bds
string PWD /mnt/lab_data/kundaje/users/oursu/code/chipseq_pipeline
string queue
int retry 0
string SHELL /bin/bash
string SHLVL 2
string SSH_CLIENT 171.66.16.89 62920 22
string SSH_CONNECTION 171.66.16.89 62920 171.65.76.244 22
string SSH_TTY /dev/pts/62
string STY 28161.test2.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 USER oursu
string UTIL_SCRIPTS_DIR /mnt/lab_data/kundaje/users/oursu/code/av_scripts/
int walltimeout 8640000
int week 604800
string WINDOW 0
string XDG_RUNTIME_DIR /run/user/1029
string XDG_SESSION_ID 47987
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt