Script file	/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20210825_173122_169
Start time	2021-08-25 17:31:22
Run time	01:32:16.581
Tasks executed	16
Tasks failed	0
Tasks failed names
Arguments*	[-type, histone, -out_dir, /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken, -title, rbc_h5, -pe, -species, galGal5, -system, local, -nth, 23, -bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken/Chickseq/RBC_I_rep1.sort.bam, -ctl_bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken/Chickseq/RBC_I_contrl.sort.bam]
System*	local
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20210825_173122_169/task.postalign_bam.jsd.line_812.id_10 chipseq.bds.20210825_173122_169/task.callpeak_macs2_chipseq.macs2_n_s_rep1.line_87.id_11 chipseq.bds.20210825_173122_169/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_87.id_12 chipseq.bds.20210825_173122_169/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_87.id_13 chipseq.bds.20210825_173122_169/task.callpeak_naive_overlap.naive_overlap_rep1_pr.line_60.id_14 chipseq.bds.20210825_173122_169/task.sys.copy_file.line_131.id_17 chipseq.bds.20210825_173122_169/task.sys.copy_file.line_131.id_18 chipseq.bds.20210825_173122_169/task.callpeak_naive_overlap.naive_overlap_final_qc.line_196.id_19 chipseq.bds.20210825_173122_169/task.callpeak_idr.FRiP_rep1_pr.line_126.id_20 chipseq.bds.20210825_173122_169/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_27 chipseq.bds.20210825_173122_169/task.callpeak_idr.FRiP_rep1.line_126.id_28 chipseq.bds.20210825_173122_169/task.report.peak2hammock.line_461.id_31 chipseq.bds.20210825_173122_169/task.report.peak2hammock.line_461.id_32 chipseq.bds.20210825_173122_169/task.report.peak2hammock.line_461.id_33 chipseq.bds.20210825_173122_169/task.graphviz.report.line_98.id_34 chipseq.bds.20210825_173122_169/task.report.pdf2png.line_428.id_67
thread_38	thread_Root
thread_39	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.postalign_bam.jsd.line_812.id_10
Name	jsd
Thread	thread_Root
PID	21786

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2021-08-25 17:31:33
End	2021-08-25 17:39:12
Elapsed	00:07:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.bam /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.bam
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rbc_h5_jsd.png /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rbc_h5_jsd.qc
Dependencies

 
# SYS command. line 813

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 814

 plotFingerprint -b /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.bam /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.bam --JSDsample /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.bam \
			--labels rep1 ctl1 \
			--outQualityMetrics /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rbc_h5_jsd.qc \
			--minMappingQuality 30 \
			-T "Fingerprints of different samples" \
			--blackListFileName /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.blacklist.bed \
			--numberOfProcessors 4 \
			--plotFile /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rbc_h5_jsd.png

# SYS command. line 823

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (451 seconds).

Num	2
ID	task.callpeak_macs2_chipseq.macs2_n_s_rep1.line_87.id_11
Name	macs2 n/s rep1
Thread	thread_Root
PID	24923

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 17:39:14
End	2021-08-25 18:56:05
Elapsed	01:16:51
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bw /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 89

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 90

 export LC_COLLATE=C

# SYS command. line 95

 macs2 callpeak -t /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz -c /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz -f BED -n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign -g 1.3e9 -p 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR 

# SYS command. line 98

 sort -k 8gr,8gr "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; print $0}' > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp

# SYS command. line 99

 head -n 500K /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp | gzip -nc > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz

# SYS command. line 100

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp

# SYS command. line 103

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.xls \
			"/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.narrowPeak \
			"/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_summits.bed

# SYS command. line 107

 if [[ true == "false" ]]; then \
			rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0; \
			exit; \
		fi

# SYS command. line 117

 macs2 bdgcmp -t "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg -c "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg --outdir /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1 -o "RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 120

 slopBed -i "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 121

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg

# SYS command. line 124

 sort -S 4G -k1,1 -k2,2n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 125

 bedGraphToBigWig /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bw

# SYS command. line 126

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 132

 chipReads=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 134

 controlReads=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.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 136

 macs2 bdgcmp -t "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg -c "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg --outdir /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1 -o "RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 139

 slopBed -i "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 140

 rm -rf "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg

# SYS command. line 143

 sort -S 4G -k1,1 -k2,2n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 144

 bedGraphToBigWig /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bw

# SYS command. line 145

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 147

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 149

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (4606 seconds).

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Aug 2021 18:39:21: 
# Command line: callpeak -t /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz -c /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz -f BED -n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign -g 1.3e9 -p 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz']
# control file = ['/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz']
# effective genome size = 1.30e+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
# Paired-End mode is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Aug 2021 18:39:21: #1 read tag files... 
INFO  @ Wed, 25 Aug 2021 18:39:21: #1 read treatment tags... 
INFO  @ Wed, 25 Aug 2021 18:39:24:  1000000 
INFO  @ Wed, 25 Aug 2021 18:39:25:  2000000 
INFO  @ Wed, 25 Aug 2021 18:39:27:  3000000 
INFO  @ Wed, 25 Aug 2021 18:39:28:  4000000 
INFO  @ Wed, 25 Aug 2021 18:39:29:  5000000 
INFO  @ Wed, 25 Aug 2021 18:39:31:  6000000 
INFO  @ Wed, 25 Aug 2021 18:39:32:  7000000 
INFO  @ Wed, 25 Aug 2021 18:39:33:  8000000 
INFO  @ Wed, 25 Aug 2021 18:39:34:  9000000 
INFO  @ Wed, 25 Aug 2021 18:39:36:  10000000 
INFO  @ Wed, 25 Aug 2021 18:39:37:  11000000 
INFO  @ Wed, 25 Aug 2021 18:39:38:  12000000 
INFO  @ Wed, 25 Aug 2021 18:39:40:  13000000 
INFO  @ Wed, 25 Aug 2021 18:39:41:  14000000 
INFO  @ Wed, 25 Aug 2021 18:39:42:  15000000 
INFO  @ Wed, 25 Aug 2021 18:39:43:  16000000 
INFO  @ Wed, 25 Aug 2021 18:39:45:  17000000 
INFO  @ Wed, 25 Aug 2021 18:39:46:  18000000 
INFO  @ Wed, 25 Aug 2021 18:39:47:  19000000 
INFO  @ Wed, 25 Aug 2021 18:39:49:  20000000 
INFO  @ Wed, 25 Aug 2021 18:39:50:  21000000 
INFO  @ Wed, 25 Aug 2021 18:39:51:  22000000 
INFO  @ Wed, 25 Aug 2021 18:39:52:  23000000 
INFO  @ Wed, 25 Aug 2021 18:39:54:  24000000 
INFO  @ Wed, 25 Aug 2021 18:39:55:  25000000 
INFO  @ Wed, 25 Aug 2021 18:39:56:  26000000 
INFO  @ Wed, 25 Aug 2021 18:39:58:  27000000 
INFO  @ Wed, 25 Aug 2021 18:39:59:  28000000 
INFO  @ Wed, 25 Aug 2021 18:40:00:  29000000 
INFO  @ Wed, 25 Aug 2021 18:40:01:  30000000 
INFO  @ Wed, 25 Aug 2021 18:40:03:  31000000 
INFO  @ Wed, 25 Aug 2021 18:40:04:  32000000 
INFO  @ Wed, 25 Aug 2021 18:40:05:  33000000 
INFO  @ Wed, 25 Aug 2021 18:40:06:  34000000 
INFO  @ Wed, 25 Aug 2021 18:40:08:  35000000 
INFO  @ Wed, 25 Aug 2021 18:40:09:  36000000 
INFO  @ Wed, 25 Aug 2021 18:40:10:  37000000 
INFO  @ Wed, 25 Aug 2021 18:40:12:  38000000 
INFO  @ Wed, 25 Aug 2021 18:40:13:  39000000 
INFO  @ Wed, 25 Aug 2021 18:40:14:  40000000 
INFO  @ Wed, 25 Aug 2021 18:40:15:  41000000 
INFO  @ Wed, 25 Aug 2021 18:40:17:  42000000 
INFO  @ Wed, 25 Aug 2021 18:40:18:  43000000 
INFO  @ Wed, 25 Aug 2021 18:40:19:  44000000 
INFO  @ Wed, 25 Aug 2021 18:40:21:  45000000 
INFO  @ Wed, 25 Aug 2021 18:40:22:  46000000 
INFO  @ Wed, 25 Aug 2021 18:40:23:  47000000 
INFO  @ Wed, 25 Aug 2021 18:40:24:  48000000 
INFO  @ Wed, 25 Aug 2021 18:40:26:  49000000 
INFO  @ Wed, 25 Aug 2021 18:40:27:  50000000 
INFO  @ Wed, 25 Aug 2021 18:40:28:  51000000 
INFO  @ Wed, 25 Aug 2021 18:40:30:  52000000 
INFO  @ Wed, 25 Aug 2021 18:40:31:  53000000 
INFO  @ Wed, 25 Aug 2021 18:40:32:  54000000 
INFO  @ Wed, 25 Aug 2021 18:40:33:  55000000 
INFO  @ Wed, 25 Aug 2021 18:40:35:  56000000 
INFO  @ Wed, 25 Aug 2021 18:40:36:  57000000 
INFO  @ Wed, 25 Aug 2021 18:40:37:  58000000 
INFO  @ Wed, 25 Aug 2021 18:40:38:  59000000 
INFO  @ Wed, 25 Aug 2021 18:40:40:  60000000 
INFO  @ Wed, 25 Aug 2021 18:40:41:  61000000 
INFO  @ Wed, 25 Aug 2021 18:40:42:  62000000 
INFO  @ Wed, 25 Aug 2021 18:40:44:  63000000 
INFO  @ Wed, 25 Aug 2021 18:40:45:  64000000 
INFO  @ Wed, 25 Aug 2021 18:40:46:  65000000 
INFO  @ Wed, 25 Aug 2021 18:40:47:  66000000 
INFO  @ Wed, 25 Aug 2021 18:40:49:  67000000 
INFO  @ Wed, 25 Aug 2021 18:40:50:  68000000 
INFO  @ Wed, 25 Aug 2021 18:40:51:  69000000 
INFO  @ Wed, 25 Aug 2021 18:40:53:  70000000 
INFO  @ Wed, 25 Aug 2021 18:40:57: #1.2 read input tags... 
INFO  @ Wed, 25 Aug 2021 18:40:59:  1000000 
INFO  @ Wed, 25 Aug 2021 18:41:00:  2000000 
INFO  @ Wed, 25 Aug 2021 18:41:01:  3000000 
INFO  @ Wed, 25 Aug 2021 18:41:03:  4000000 
INFO  @ Wed, 25 Aug 2021 18:41:04:  5000000 
INFO  @ Wed, 25 Aug 2021 18:41:05:  6000000 
INFO  @ Wed, 25 Aug 2021 18:41:07:  7000000 
INFO  @ Wed, 25 Aug 2021 18:41:08:  8000000 
INFO  @ Wed, 25 Aug 2021 18:41:09:  9000000 
INFO  @ Wed, 25 Aug 2021 18:41:10:  10000000 
INFO  @ Wed, 25 Aug 2021 18:41:12:  11000000 
INFO  @ Wed, 25 Aug 2021 18:41:13:  12000000 
INFO  @ Wed, 25 Aug 2021 18:41:14:  13000000 
INFO  @ Wed, 25 Aug 2021 18:41:16:  14000000 
INFO  @ Wed, 25 Aug 2021 18:41:17:  15000000 
INFO  @ Wed, 25 Aug 2021 18:41:18:  16000000 
INFO  @ Wed, 25 Aug 2021 18:41:19:  17000000 
INFO  @ Wed, 25 Aug 2021 18:41:21:  18000000 
INFO  @ Wed, 25 Aug 2021 18:41:22:  19000000 
INFO  @ Wed, 25 Aug 2021 18:41:23:  20000000 
INFO  @ Wed, 25 Aug 2021 18:41:25:  21000000 
INFO  @ Wed, 25 Aug 2021 18:41:26:  22000000 
INFO  @ Wed, 25 Aug 2021 18:41:27:  23000000 
INFO  @ Wed, 25 Aug 2021 18:41:28:  24000000 
INFO  @ Wed, 25 Aug 2021 18:41:30:  25000000 
INFO  @ Wed, 25 Aug 2021 18:41:31:  26000000 
INFO  @ Wed, 25 Aug 2021 18:41:32:  27000000 
INFO  @ Wed, 25 Aug 2021 18:41:34:  28000000 
INFO  @ Wed, 25 Aug 2021 18:41:35:  29000000 
INFO  @ Wed, 25 Aug 2021 18:41:38: #1 tag size is determined as 151 bps 
INFO  @ Wed, 25 Aug 2021 18:41:38: #1 tag size = 151 
INFO  @ Wed, 25 Aug 2021 18:41:38: #1  total tags in treatment: 70040480 
INFO  @ Wed, 25 Aug 2021 18:41:38: #1  total tags in control: 29912794 
INFO  @ Wed, 25 Aug 2021 18:41:38: #1 finished! 
INFO  @ Wed, 25 Aug 2021 18:41:38: #2 Build Peak Model... 
INFO  @ Wed, 25 Aug 2021 18:41:38: #2 Skipped... 
INFO  @ Wed, 25 Aug 2021 18:41:38: #2 Use 200 as fragment length 
INFO  @ Wed, 25 Aug 2021 18:41:38: #3 Call peaks... 
INFO  @ Wed, 25 Aug 2021 18:41:38: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Aug 2021 18:41:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Aug 2021 18:44:22: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Aug 2021 18:44:22: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Aug 2021 18:44:22: #3   Write bedGraph files for control lambda (after scaling if necessary)... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Aug 2021 18:44:22: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Aug 2021 18:44:22: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Aug 2021 18:50:52: #4 Write output xls file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Aug 2021 18:50:52: #4 Write peak in narrowPeak format file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Aug 2021 18:50:52: #4 Write summits bed file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Aug 2021 18:50:52: Done! 
INFO  @ Wed, 25 Aug 2021 18:50:53: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Aug 2021 18:52:49: Read and build control bedGraph... 
INFO  @ Wed, 25 Aug 2021 18:53:48: Build scoreTrackII... 
INFO  @ Wed, 25 Aug 2021 18:54:37: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Aug 2021 19:01:22: Write bedGraph of scores... 
INFO  @ Wed, 25 Aug 2021 19:06:21: Finished 'FE'! Please check '/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Aug 2021 19:26:49: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Aug 2021 19:28:45: Read and build control bedGraph... 
INFO  @ Wed, 25 Aug 2021 19:29:44: Build scoreTrackII... 
INFO  @ Wed, 25 Aug 2021 19:30:34: Values in your input bedGraph files will be multiplied by 29.912794 ... 
INFO  @ Wed, 25 Aug 2021 19:36:58: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Aug 2021 19:37:45: Write bedGraph of scores... 
INFO  @ Wed, 25 Aug 2021 19:41:08: Finished 'ppois'! Please check '/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_ppois.bdg'!

Num	3
ID	task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_87.id_12
Name	macs2 n/s rep1-pr1
Thread	thread_Root
PID	24949

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 17:39:15
End	2021-08-25 17:47:38
Elapsed	00:08:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
Dependencies

 
# SYS command. line 89

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 90

 export LC_COLLATE=C

# SYS command. line 95

 macs2 callpeak -t /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign.gz -c /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz -f BED -n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign -g 1.3e9 -p 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR 

# SYS command. line 98

 sort -k 8gr,8gr "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; print $0}' > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp

# SYS command. line 99

 head -n 500K /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp | gzip -nc > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz

# SYS command. line 100

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp

# SYS command. line 103

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.xls \
			"/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.narrowPeak \
			"/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_summits.bed

# SYS command. line 107

 if [[ false == "false" ]]; then \
			rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0; \
			exit; \
		fi

# SYS command. line 117

 macs2 bdgcmp -t "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg -c "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg --outdir /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1 -o "RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 120

 slopBed -i "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 121

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg

# SYS command. line 124

 sort -S 4G -k1,1 -k2,2n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 125

 bedGraphToBigWig /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bw

# SYS command. line 126

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 132

 chipReads=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 134

 controlReads=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.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 136

 macs2 bdgcmp -t "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg -c "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg --outdir /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1 -o "RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 139

 slopBed -i "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 140

 rm -rf "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg

# SYS command. line 143

 sort -S 4G -k1,1 -k2,2n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 144

 bedGraphToBigWig /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bw

# SYS command. line 145

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 147

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 149

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (497 seconds).

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Aug 2021 18:39:21: 
# Command line: callpeak -t /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign.gz -c /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz -f BED -n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign -g 1.3e9 -p 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign.gz']
# control file = ['/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz']
# effective genome size = 1.30e+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
# Paired-End mode is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Aug 2021 18:39:21: #1 read tag files... 
INFO  @ Wed, 25 Aug 2021 18:39:21: #1 read treatment tags... 
INFO  @ Wed, 25 Aug 2021 18:39:24:  1000000 
INFO  @ Wed, 25 Aug 2021 18:39:25:  2000000 
INFO  @ Wed, 25 Aug 2021 18:39:27:  3000000 
INFO  @ Wed, 25 Aug 2021 18:39:28:  4000000 
INFO  @ Wed, 25 Aug 2021 18:39:29:  5000000 
INFO  @ Wed, 25 Aug 2021 18:39:30:  6000000 
INFO  @ Wed, 25 Aug 2021 18:39:32:  7000000 
INFO  @ Wed, 25 Aug 2021 18:39:33:  8000000 
INFO  @ Wed, 25 Aug 2021 18:39:34:  9000000 
INFO  @ Wed, 25 Aug 2021 18:39:36:  10000000 
INFO  @ Wed, 25 Aug 2021 18:39:37:  11000000 
INFO  @ Wed, 25 Aug 2021 18:39:38:  12000000 
INFO  @ Wed, 25 Aug 2021 18:39:40:  13000000 
INFO  @ Wed, 25 Aug 2021 18:39:41:  14000000 
INFO  @ Wed, 25 Aug 2021 18:39:42:  15000000 
INFO  @ Wed, 25 Aug 2021 18:39:44:  16000000 
INFO  @ Wed, 25 Aug 2021 18:39:45:  17000000 
INFO  @ Wed, 25 Aug 2021 18:39:46:  18000000 
INFO  @ Wed, 25 Aug 2021 18:39:47:  19000000 
INFO  @ Wed, 25 Aug 2021 18:39:49:  20000000 
INFO  @ Wed, 25 Aug 2021 18:39:50:  21000000 
INFO  @ Wed, 25 Aug 2021 18:39:51:  22000000 
INFO  @ Wed, 25 Aug 2021 18:39:53:  23000000 
INFO  @ Wed, 25 Aug 2021 18:39:54:  24000000 
INFO  @ Wed, 25 Aug 2021 18:39:55:  25000000 
INFO  @ Wed, 25 Aug 2021 18:39:57:  26000000 
INFO  @ Wed, 25 Aug 2021 18:39:58:  27000000 
INFO  @ Wed, 25 Aug 2021 18:39:59:  28000000 
INFO  @ Wed, 25 Aug 2021 18:40:01:  29000000 
INFO  @ Wed, 25 Aug 2021 18:40:02:  30000000 
INFO  @ Wed, 25 Aug 2021 18:40:03:  31000000 
INFO  @ Wed, 25 Aug 2021 18:40:04:  32000000 
INFO  @ Wed, 25 Aug 2021 18:40:06:  33000000 
INFO  @ Wed, 25 Aug 2021 18:40:07:  34000000 
INFO  @ Wed, 25 Aug 2021 18:40:08:  35000000 
INFO  @ Wed, 25 Aug 2021 18:40:11: #1.2 read input tags... 
INFO  @ Wed, 25 Aug 2021 18:40:13:  1000000 
INFO  @ Wed, 25 Aug 2021 18:40:15:  2000000 
INFO  @ Wed, 25 Aug 2021 18:40:16:  3000000 
INFO  @ Wed, 25 Aug 2021 18:40:17:  4000000 
INFO  @ Wed, 25 Aug 2021 18:40:19:  5000000 
INFO  @ Wed, 25 Aug 2021 18:40:20:  6000000 
INFO  @ Wed, 25 Aug 2021 18:40:21:  7000000 
INFO  @ Wed, 25 Aug 2021 18:40:23:  8000000 
INFO  @ Wed, 25 Aug 2021 18:40:24:  9000000 
INFO  @ Wed, 25 Aug 2021 18:40:25:  10000000 
INFO  @ Wed, 25 Aug 2021 18:40:26:  11000000 
INFO  @ Wed, 25 Aug 2021 18:40:28:  12000000 
INFO  @ Wed, 25 Aug 2021 18:40:29:  13000000 
INFO  @ Wed, 25 Aug 2021 18:40:30:  14000000 
INFO  @ Wed, 25 Aug 2021 18:40:32:  15000000 
INFO  @ Wed, 25 Aug 2021 18:40:33:  16000000 
INFO  @ Wed, 25 Aug 2021 18:40:34:  17000000 
INFO  @ Wed, 25 Aug 2021 18:40:35:  18000000 
INFO  @ Wed, 25 Aug 2021 18:40:37:  19000000 
INFO  @ Wed, 25 Aug 2021 18:40:38:  20000000 
INFO  @ Wed, 25 Aug 2021 18:40:39:  21000000 
INFO  @ Wed, 25 Aug 2021 18:40:41:  22000000 
INFO  @ Wed, 25 Aug 2021 18:40:42:  23000000 
INFO  @ Wed, 25 Aug 2021 18:40:43:  24000000 
INFO  @ Wed, 25 Aug 2021 18:40:45:  25000000 
INFO  @ Wed, 25 Aug 2021 18:40:46:  26000000 
INFO  @ Wed, 25 Aug 2021 18:40:47:  27000000 
INFO  @ Wed, 25 Aug 2021 18:40:48:  28000000 
INFO  @ Wed, 25 Aug 2021 18:40:50:  29000000 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1 tag size is determined as 150 bps 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1 tag size = 150 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1  total tags in treatment: 35020240 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1  total tags in control: 29912794 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1 finished! 
INFO  @ Wed, 25 Aug 2021 18:40:53: #2 Build Peak Model... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #2 Skipped... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #2 Use 200 as fragment length 
INFO  @ Wed, 25 Aug 2021 18:40:53: #3 Call peaks... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Aug 2021 18:42:55: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Aug 2021 18:42:55: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Aug 2021 18:42:55: #3   Write bedGraph files for control lambda (after scaling if necessary)... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Aug 2021 18:42:55: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Aug 2021 18:42:55: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Aug 2021 18:47:35: #4 Write output xls file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Aug 2021 18:47:36: #4 Write peak in narrowPeak format file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Aug 2021 18:47:36: #4 Write summits bed file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Aug 2021 18:47:36: Done!

Num	4
ID	task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_87.id_13
Name	macs2 n/s rep1-pr2
Thread	thread_Root
PID	24999

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 17:39:16
End	2021-08-25 17:47:57
Elapsed	00:08:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
Dependencies

 
# SYS command. line 89

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 90

 export LC_COLLATE=C

# SYS command. line 95

 macs2 callpeak -t /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign.gz -c /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz -f BED -n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign -g 1.3e9 -p 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR 

# SYS command. line 98

 sort -k 8gr,8gr "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; print $0}' > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp

# SYS command. line 99

 head -n 500K /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp | gzip -nc > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz

# SYS command. line 100

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz.tmp

# SYS command. line 103

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.xls \
			"/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_peaks.narrowPeak \
			"/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_summits.bed

# SYS command. line 107

 if [[ false == "false" ]]; then \
			rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0; \
			exit; \
		fi

# SYS command. line 117

 macs2 bdgcmp -t "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg -c "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg --outdir /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2 -o "RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 120

 slopBed -i "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 121

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_FE.bdg

# SYS command. line 124

 sort -S 4G -k1,1 -k2,2n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 125

 bedGraphToBigWig /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bw

# SYS command. line 126

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bedgraph /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 132

 chipReads=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 134

 controlReads=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.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 136

 macs2 bdgcmp -t "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg -c "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg --outdir /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2 -o "RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 139

 slopBed -i "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 140

 rm -rf "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_ppois.bdg

# SYS command. line 143

 sort -S 4G -k1,1 -k2,2n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 144

 bedGraphToBigWig /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bw

# SYS command. line 145

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bedgraph /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 147

 rm -f "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_treat_pileup.bdg "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 149

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (515 seconds).

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Aug 2021 18:39:21: 
# Command line: callpeak -t /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign.gz -c /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz -f BED -n /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign -g 1.3e9 -p 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign.gz']
# control file = ['/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz']
# effective genome size = 1.30e+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
# Paired-End mode is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Aug 2021 18:39:21: #1 read tag files... 
INFO  @ Wed, 25 Aug 2021 18:39:21: #1 read treatment tags... 
INFO  @ Wed, 25 Aug 2021 18:39:24:  1000000 
INFO  @ Wed, 25 Aug 2021 18:39:25:  2000000 
INFO  @ Wed, 25 Aug 2021 18:39:26:  3000000 
INFO  @ Wed, 25 Aug 2021 18:39:28:  4000000 
INFO  @ Wed, 25 Aug 2021 18:39:29:  5000000 
INFO  @ Wed, 25 Aug 2021 18:39:30:  6000000 
INFO  @ Wed, 25 Aug 2021 18:39:32:  7000000 
INFO  @ Wed, 25 Aug 2021 18:39:33:  8000000 
INFO  @ Wed, 25 Aug 2021 18:39:34:  9000000 
INFO  @ Wed, 25 Aug 2021 18:39:36:  10000000 
INFO  @ Wed, 25 Aug 2021 18:39:37:  11000000 
INFO  @ Wed, 25 Aug 2021 18:39:38:  12000000 
INFO  @ Wed, 25 Aug 2021 18:39:40:  13000000 
INFO  @ Wed, 25 Aug 2021 18:39:41:  14000000 
INFO  @ Wed, 25 Aug 2021 18:39:42:  15000000 
INFO  @ Wed, 25 Aug 2021 18:39:44:  16000000 
INFO  @ Wed, 25 Aug 2021 18:39:45:  17000000 
INFO  @ Wed, 25 Aug 2021 18:39:46:  18000000 
INFO  @ Wed, 25 Aug 2021 18:39:48:  19000000 
INFO  @ Wed, 25 Aug 2021 18:39:49:  20000000 
INFO  @ Wed, 25 Aug 2021 18:39:50:  21000000 
INFO  @ Wed, 25 Aug 2021 18:39:51:  22000000 
INFO  @ Wed, 25 Aug 2021 18:39:53:  23000000 
INFO  @ Wed, 25 Aug 2021 18:39:54:  24000000 
INFO  @ Wed, 25 Aug 2021 18:39:55:  25000000 
INFO  @ Wed, 25 Aug 2021 18:39:57:  26000000 
INFO  @ Wed, 25 Aug 2021 18:39:58:  27000000 
INFO  @ Wed, 25 Aug 2021 18:39:59:  28000000 
INFO  @ Wed, 25 Aug 2021 18:40:01:  29000000 
INFO  @ Wed, 25 Aug 2021 18:40:02:  30000000 
INFO  @ Wed, 25 Aug 2021 18:40:03:  31000000 
INFO  @ Wed, 25 Aug 2021 18:40:05:  32000000 
INFO  @ Wed, 25 Aug 2021 18:40:06:  33000000 
INFO  @ Wed, 25 Aug 2021 18:40:07:  34000000 
INFO  @ Wed, 25 Aug 2021 18:40:09:  35000000 
INFO  @ Wed, 25 Aug 2021 18:40:11: #1.2 read input tags... 
INFO  @ Wed, 25 Aug 2021 18:40:13:  1000000 
INFO  @ Wed, 25 Aug 2021 18:40:15:  2000000 
INFO  @ Wed, 25 Aug 2021 18:40:16:  3000000 
INFO  @ Wed, 25 Aug 2021 18:40:17:  4000000 
INFO  @ Wed, 25 Aug 2021 18:40:19:  5000000 
INFO  @ Wed, 25 Aug 2021 18:40:20:  6000000 
INFO  @ Wed, 25 Aug 2021 18:40:21:  7000000 
INFO  @ Wed, 25 Aug 2021 18:40:23:  8000000 
INFO  @ Wed, 25 Aug 2021 18:40:24:  9000000 
INFO  @ Wed, 25 Aug 2021 18:40:25:  10000000 
INFO  @ Wed, 25 Aug 2021 18:40:27:  11000000 
INFO  @ Wed, 25 Aug 2021 18:40:28:  12000000 
INFO  @ Wed, 25 Aug 2021 18:40:29:  13000000 
INFO  @ Wed, 25 Aug 2021 18:40:31:  14000000 
INFO  @ Wed, 25 Aug 2021 18:40:32:  15000000 
INFO  @ Wed, 25 Aug 2021 18:40:33:  16000000 
INFO  @ Wed, 25 Aug 2021 18:40:34:  17000000 
INFO  @ Wed, 25 Aug 2021 18:40:36:  18000000 
INFO  @ Wed, 25 Aug 2021 18:40:37:  19000000 
INFO  @ Wed, 25 Aug 2021 18:40:38:  20000000 
INFO  @ Wed, 25 Aug 2021 18:40:40:  21000000 
INFO  @ Wed, 25 Aug 2021 18:40:41:  22000000 
INFO  @ Wed, 25 Aug 2021 18:40:42:  23000000 
INFO  @ Wed, 25 Aug 2021 18:40:44:  24000000 
INFO  @ Wed, 25 Aug 2021 18:40:45:  25000000 
INFO  @ Wed, 25 Aug 2021 18:40:46:  26000000 
INFO  @ Wed, 25 Aug 2021 18:40:48:  27000000 
INFO  @ Wed, 25 Aug 2021 18:40:49:  28000000 
INFO  @ Wed, 25 Aug 2021 18:40:50:  29000000 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1 tag size is determined as 149 bps 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1 tag size = 149 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1  total tags in treatment: 35020240 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1  total tags in control: 29912794 
INFO  @ Wed, 25 Aug 2021 18:40:53: #1 finished! 
INFO  @ Wed, 25 Aug 2021 18:40:53: #2 Build Peak Model... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #2 Skipped... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #2 Use 200 as fragment length 
INFO  @ Wed, 25 Aug 2021 18:40:53: #3 Call peaks... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Aug 2021 18:40:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Aug 2021 18:43:09: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Aug 2021 18:43:09: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Aug 2021 18:43:09: #3   Write bedGraph files for control lambda (after scaling if necessary)... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Aug 2021 18:43:09: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Aug 2021 18:43:09: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Aug 2021 18:47:54: #4 Write output xls file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Aug 2021 18:47:55: #4 Write peak in narrowPeak format file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Aug 2021 18:47:55: #4 Write summits bed file... /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Aug 2021 18:47:55: Done!

Num	5
ID	task.callpeak_naive_overlap.naive_overlap_rep1_pr.line_60.id_14
Name	naive_overlap rep1-pr
Thread	thread_Root
PID	23931

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 18:56:07
End	2021-08-25 18:56:13
Elapsed	00:00:06
Timeout	01:00:00
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 62

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 65

 intersectBed  -wo -a <(zcat -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz) -b <(zcat -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.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 /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.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 > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 71

 zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.narrowPeak.gz

# SYS command. line 73

 bedtools intersect -v -a <(zcat -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.narrowPeak.gz) -b <(zcat -f /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.blacklist.bed)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz

# SYS command. line 75

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 77

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (0 seconds).

Num	6
ID	task.sys.copy_file.line_131.id_17
Name	copy file
Thread	thread_Root
PID	24024

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 18:56:14
End	2021-08-25 18:56:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	7
ID	task.sys.copy_file.line_131.id_18
Name	copy file
Thread	thread_Root
PID	24030

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 18:56:15
End	2021-08-25 18:56:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 133

 cp --remove-destination /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	8
ID	task.callpeak_naive_overlap.naive_overlap_final_qc.line_196.id_19
Name	naive overlap final qc
Thread	thread_Root
PID	24071

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 18:56:17
End	2021-08-25 18:56:22
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rbc_h5_peak_overlap_final.qc
Dependencies

 
# SYS command. line 198

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 200

 echo -e "Nt\tN1	N2	""Np\tN_opt\tN_consv\topt_set\tconsv_set\trescue_ratio\tself_consistency_ratio\treproducibility_test" > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rbc_h5_peak_overlap_final.qc

# SYS command. line 201

 echo -e "0\t5904	0	""0\t5904\t5904\tself_pseudo_rep_rep1\tself_pseudo_rep_rep1\t0.0\t1.0\tpass" >> /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rbc_h5_peak_overlap_final.qc

# SYS command. line 203

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (0 seconds).

Num	9
ID	task.callpeak_idr.FRiP_rep1_pr.line_126.id_20
Name	FRiP rep1-pr
Thread	thread_Root
PID	24097

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 18:56:18
End	2021-08-25 18:59:33
Elapsed	00:03:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.FRiP.qc
Dependencies

 
# SYS command. line 127

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 129

 val1=$(bedtools slop -i /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -s -l -100 -r 100 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b <(zcat -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz) -wa -u | wc -l)

# SYS command. line 139

 val2=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz | wc -l)

# SYS command. line 140

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.FRiP.qc

# SYS command. line 141

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (189 seconds).

Num	10
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_27
Name	blacklist_filter peak 1
Thread	thread_Root
PID	25533

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 18:59:35
End	2021-08-25 18:59:41
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 31

 bedtools intersect -v -a <(zcat -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz) -b <(zcat -f /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.blacklist.bed) \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (1 seconds).

Num	11
ID	task.callpeak_idr.FRiP_rep1.line_126.id_28
Name	FRiP rep1
Thread	thread_Root
PID	25598

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 18:59:41
End	2021-08-25 19:03:09
Elapsed	00:03:27
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.filt.narrowPeak.FRiP.qc
Dependencies	blacklist_filter peak 1 blacklist_filter peak 1

 
# SYS command. line 127

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 129

 val1=$(bedtools slop -i /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz -g /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken/galGal5.chrom.sizes -s -l -100 -r 100 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b <(zcat -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.filt.narrowPeak.gz) -wa -u | wc -l)

# SYS command. line 139

 val2=$(zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz | wc -l)

# SYS command. line 140

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.filt.narrowPeak.FRiP.qc

# SYS command. line 141

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

   
--------------------Stdout--------------------
Task has finished (203 seconds).

Num	12
ID	task.report.peak2hammock.line_461.id_31
Name	peak2hammock
Thread	thread_Root
PID	27066

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 19:03:10
End	2021-08-25 19:03:15
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 463

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 464

 zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 466

 /mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils/narrowpeak.py /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 467

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp

Num	13
ID	task.report.peak2hammock.line_461.id_32
Name	peak2hammock
Thread	thread_Root
PID	27151

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 19:03:16
End	2021-08-25 19:03:22
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 463

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 464

 zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 466

 /mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils/narrowpeak.py /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 467

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp

Num	14
ID	task.report.peak2hammock.line_461.id_33
Name	peak2hammock
Thread	thread_Root
PID	27261

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 19:03:23
End	2021-08-25 19:03:28
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 463

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 464

 zcat /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 466

 /mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils/narrowpeak.py /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 467

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.tmp

Num	15
ID	task.graphviz.report.line_98.id_34
Name	report
Thread	thread_Root
PID	27383

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 19:03:29
End	2021-08-25 19:03:38
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 99

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 100

 dot -Tsvg /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/report/rbc_h5_workflow.dot > /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/report/rbc_h5_workflow.svg 2> /dev/null || echo "svg: /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/report/rbc_h5_workflow.svg" # to suppress dot font error (exit code=1)

Num	16
ID	task.report.pdf2png.line_428.id_67
Name	pdf2png
Thread	thread_Root
PID	27509

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2021-08-25 19:03:30
End	2021-08-25 19:03:36
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.plot.pdf
Output files	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.plot.png
Dependencies

 
# SYS command. line 429

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 430

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.plot.png \
			-r144 /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.plot.pdf

Type	Name	Value
string	_	/mnt/storage/home/psbelokopytova/insulatory_index/.bds/bds
string	_LMFILES_	/opt/shared/modules/jre/1.8.0
string	_ModuleTable001_	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
string	_ModuleTable002_	Yi9tb2R1bGVmaWxlczovdXNyL3NoYXJlL2xtb2QvbW9kdWxlZmlsZXM6L29wdC9zaGFyZWQvbW9kdWxlcyIsfQ==
string	_ModuleTable_Sz_	2
bool	allowEmpty	false
string	ALSA_CONFIG_PATH	/etc/alsa-pulse.conf
string	ANSOFT_LICENSE_FILE	1055@vm-ansys
string	ANSYSLMD_LICENSE_FILE	1055@vm-ansys
string[]	args	[-type, histone, -out_dir, /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken, -title, rbc_h5, -pe, -species, galGal5, -system, local, -nth, 23, -bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken/Chickseq/RBC_I_rep1.sort.bam, -ctl_bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken/Chickseq/RBC_I_contrl.sort.bam]
string	AUDIODRIVER	pulseaudio
string	BASH_ENV	/usr/share/lmod/7.6.1/init/bash
string	BASH_FUNC_mc%%	() { . /usr/share/mc/mc-wrapper.sh\n}
string	BASH_FUNC_ml%%	() { eval $($LMOD_DIR/ml_cmd \"$@\")\n}
string	BASH_FUNC_module%%	() { eval $($LMOD_CMD bash \"$@\") && eval $(${LMOD_SETTARG_CMD:-:} -s sh)\n}
bool	canFail	false
string	COLORTERM	1
string	CPU	x86_64
int	cpus	-1
int	cpusLocal	24
string	CSHEDIT	emacs
string	CVS_RSH	ssh
int	day	86400
real	E	2.718281828459045
string	ENVIRONMENT	BATCH
string	FROM_HEADER
string	ftp_proxy	http://proxy.hpc.nusc.ru:8080
int	G	1073741824
string	G_BROKEN_FILENAMES	1
string	G_FILENAME_ENCODING	@locale,UTF-8,ISO-8859-15,CP1252
string	gopher_proxy
string	GPG_TTY	not a tty
string	HISTSIZE	1000
string	HOME	/mnt/storage/home/psbelokopytova
string	HOST	cn303
string	HOSTNAME	cn303
string	HOSTTYPE	x86_64
int	hour	3600
string	http_proxy	http://proxy.hpc.nusc.ru:8080
string	https_proxy	http://proxy.hpc.nusc.ru:8080
string	INPUTRC	/mnt/storage/home/psbelokopytova/.inputrc
string	INTEL_LICENSE_FILE	28519@hpc-suvir1,28519@hpc-suvir2,28519@srpo
string	JAVA_HOME	/opt/shared/java/jre1.8.0_45
int	K	1024
string	LANG	en_US.UTF-8
string	LESS	-M -I -R
string	LESS_ADVANCED_PREPROCESSOR	no
string	LESSCLOSE	lessclose.sh %s %s
string	LESSKEY	/etc/lesskey.bin
string	LESSOPEN	lessopen.sh %s
string	LMOD_CMD	/usr/share/lmod/lmod/libexec/lmod
string	LMOD_COLORIZE	no
string	LMOD_DIR	/usr/share/lmod/lmod/libexec
string	LMOD_FULL_SETTARG_SUPPORT	no
string	LMOD_PKG	/usr/share/lmod/lmod
string	LMOD_PREPEND_BLOCK	normal
string	LMOD_SETTARG_CMD	:
string	LMOD_VERSION	7.6.1
string	LOADEDMODULES	jre/1.8.0
string	LOGNAME	psbelokopytova
int	M	1048576
string	MACHTYPE	x86_64-suse-linux
string	MAIL	/var/spool/mail/psbelokopytova
string	MANPATH	/usr/local/man:/usr/local/share/man:/usr/share/man:/usr/man:/opt/pbs/share/man
int	mem	-1
string	MINICOM	-c on
int	minute	60
string	MLM_LICENSE_FILE	27000@hpc-suvir1,27000@hpc-suvir2,27000@srpo
string	MODULEPATH	/opt/ohpc/pub/modulefiles:/usr/share/lmod/modulefiles:/opt/shared/modules
string	MODULESHOME	/usr/share/lmod/lmod
string	MORE	-sl
string	MSC_LICENSE_FILE	1700@hpc-suvir1,1700@hpc-suvir2,1700@srpo
string	NCPUS	24
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	NNTPSERVER	news
string	NO_PROXY	localhost, 127.0.0.1, hpc.nusc.ru
string	no_proxy	localhost, 127.0.0.1, hpc.nusc.ru
string	node
string	OMP_NUM_THREADS	24
string	OSTYPE	linux
int	P	1125899906842624
string	PAGER	less
string	PATH	/opt/shared/java/jre1.8.0_45/bin:/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin:/mnt/storage/home/psbelokopytova/bin:/mnt/storage/home/psbelokopytova/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/opt/shared/bin:/opt/pbs/bin:/mnt/storage/home/psbelokopytova/insulatory_index/.bds
string	PBS_ENVIRONMENT	PBS_BATCH
string	PBS_JOBCOOKIE	751389C11B1B98781957810828C55564
string	PBS_JOBDIR	/mnt/storage/home/psbelokopytova
string	PBS_JOBID	3520037.vm-pbs
string	PBS_JOBNAME	aquas_rbc_h5.sh
string	PBS_MOMPORT	15003
string	PBS_NODEFILE	/var/spool/pbs/aux/3520037.vm-pbs
string	PBS_NODENUM	0
string	PBS_O_HOME	/mnt/storage/home/psbelokopytova
string	PBS_O_HOST	clu.hpc.nusc.ru
string	PBS_O_LANG	en_US.UTF-8
string	PBS_O_LOGNAME	psbelokopytova
string	PBS_O_MAIL	/var/mail/psbelokopytova
string	PBS_O_PATH	/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin:/mnt/storage/home/psbelokopytova/bin/:/mnt/storage/home/psbelokopytova/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/shared/bin:/opt/pbs/bin:/mnt/storage/home/psbelokopytova/insulatory_index/.bds/
string	PBS_O_QUEUE	xl230g9q
string	PBS_O_SHELL	/bin/bash
string	PBS_O_SYSTEM	Linux
string	PBS_O_WORKDIR	/mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken
string	PBS_QUEUE	xl230g9_middle
string	PBS_TASKNUM	1
real	PI	3.141592653589793
string	ppwd	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken
string	PROFILEREAD	true
string	programName	chipseq.bds
string	programPath	/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/chipseq.bds
string	PWD	/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken
string	PYTHONSTARTUP	/etc/pythonstart
string	QEMU_AUDIO_DRV	pa
string	QT_SYSTEM_DIR	/usr/share/desktop-data
string	queue
int	retry	0
string	SDL_AUDIODRIVER	pulse
string	SHELL	/bin/bash
string	SHLVL	3
string	SOCKS5_SERVER
string	SOCKS_PROXY
string	socks_proxy
string	system	local
int	T	1099511627776
int	timeout	-1
string	TMPDIR	/var/tmp/pbs.3520037.vm-pbs
string	TZ	Asia/Novosibirsk
string	USER	psbelokopytova
int	walltimeout	8640000
int	week	604800
string	WINDOWMANAGER	env GNOME_SHELL_SESSION_MODE=classic SLE_CLASSIC_MODE=1 gnome-session --session gnome-classic
string	XCURSOR_THEME	DMZ
string	XDG_CONFIG_DIRS	/etc/xdg
string	XDG_DATA_DIRS	/usr/share
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt
string	XKEYSYMDB	/usr/X11R6/lib/X11/XKeysymDB
string	XNLSPATH	/usr/share/X11/nls

BigDataScript report: chipseq.bds

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