2021-08-27 02:45:37,100 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179589' --- 2021-08-27 02:45:37,100 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179589.sra 2021-08-27 02:45:37,100 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__ 2021-08-27 02:45:37,100 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpmn5c713v "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179589.sra" 2021-08-27 03:21:28,067 INFO SimpleSubprocess Sra2FastQ - 0:35:50 2021-08-27 03:21:28,077 DEBUG SimpleSubprocess gzip /tmp/tmpmn5c713v/* 2021-08-27 06:21:27,947 INFO SimpleSubprocess GZipFastQ - 2:59:59 2021-08-27 06:21:27,985 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/fastq"; mv /tmp/tmpmn5c713v/SRR3179589_2.fastq.gz /tmp/tmpmn5c713v/SRR3179589_R2.fastq.gz; mv /tmp/tmpmn5c713v/SRR3179589_1.fastq.gz /tmp/tmpmn5c713v/SRR3179589_R1.fastq.gz; cp /tmp/tmpmn5c713v/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/fastq" 2021-08-27 06:25:45,192 INFO SimpleSubprocess CopyFiles - 0:04:17 2021-08-27 06:25:47,092 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__ 2021-08-27 06:25:47,092 INFO Juicer Genome assembly: mm10 2021-08-27 06:25:47,092 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-27 06:25:47,093 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 06:25:47,093 INFO Juicer Enzyme: DpnII 2021-08-27 06:25:47,093 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-27 06:25:47,093 INFO Juicer Threads: 10 2021-08-27 06:25:47,093 DEBUG SimpleSubprocess bash "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/juicer.sh" -t 10 -D "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer" -g mm10 -z "/Data/DataBases/mm10/mm10_canonic.fa" -p "/Data/DataBases/mm10/mm10_canonic.chrom.sizes" -s DpnII -y "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt" -d "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__" 2021-08-27 15:49:19,994 INFO SimpleSubprocess Juicer - 9:23:32 2021-08-27 15:49:20,015 INFO Juicer Using /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt as site file (-: Looking for fastq files...fastq files exist (-: Aligning files matching /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/fastq/*_R*.fastq* to genome mm10 with site file /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt (-: Created /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/splits/SRR3179589_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/splits/SRR3179589_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/splits/SRR3179589.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/splits/SRR3179589.fastq.gz.sam done successfully (-: Finished sorting all sorted files into a single merge. WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-27T14:43:56,639] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body ........................................................................................................................................................................................................................................ Writing footer Finished preprocess Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Finished writing norms WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-27T15:23:41,637] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body ........................................................................................................................................................................................................................................ Writing footer Finished preprocess Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Finished writing norms /Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools is post-processing Hi-C for mm10 Data read from /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_30.hic. Motifs read from /Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/references/motif ARROWHEAD: WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-27T15:49:19,579] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_30.hic Using 1 CPU thread(s) HiCCUPS: GPUs are not installed so HiCCUPs cannot be run (-: Postprocessing successfully completed, maps too sparse to annotate or GPUs unavailable (-: (-: Pipeline successfully completed (-: Run cleanup.sh to remove the splits directory Check /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned for results 2021-08-27 15:49:20,025 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/merged_nodups.txt 2021-08-27 15:49:20,025 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt 2021-08-27 15:49:20,026 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp84kx41f5/inter.pairs.txt" 2021-08-27 15:50:31,218 INFO SimpleSubprocess MakeInterPairs - 0:01:11 2021-08-27 15:50:31,218 DEBUG SimpleSubprocess cp "/tmp/tmp84kx41f5/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt" 2021-08-27 15:50:33,077 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-27 15:50:33,329 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt 2021-08-27 15:50:33,329 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-27 15:50:33,329 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 15:50:33,329 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 15:50:33,329 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-27 15:50:33,369 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":5000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt" "/tmp/tmpzvlva82w/inter_no_balanced.cool" 2021-08-27 15:52:14,278 INFO SimpleSubprocess MakeCool - 0:01:40 2021-08-27 15:52:14,279 DEBUG SimpleSubprocess cp "/tmp/tmpzvlva82w/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-27 15:52:14,311 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:52:14,361 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt 2021-08-27 15:52:14,361 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-27 15:52:14,361 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 15:52:14,361 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 15:52:14,361 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-27 15:52:14,387 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":10000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt" "/tmp/tmpl959g563/inter_no_balanced.cool" 2021-08-27 15:53:39,891 INFO SimpleSubprocess MakeCool - 0:01:25 2021-08-27 15:53:39,891 DEBUG SimpleSubprocess cp "/tmp/tmpl959g563/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-27 15:53:39,915 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:53:39,919 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt 2021-08-27 15:53:39,919 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-27 15:53:39,919 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 15:53:39,919 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 15:53:39,919 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-27 15:53:39,919 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":20000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt" "/tmp/tmph81amg02/inter_no_balanced.cool" 2021-08-27 15:55:03,292 INFO SimpleSubprocess MakeCool - 0:01:23 2021-08-27 15:55:03,292 DEBUG SimpleSubprocess cp "/tmp/tmph81amg02/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-27 15:55:03,315 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:55:03,318 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt 2021-08-27 15:55:03,318 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-27 15:55:03,318 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 15:55:03,318 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 15:55:03,318 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-27 15:55:03,342 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":25000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt" "/tmp/tmpq0n8z0j5/inter_no_balanced.cool" 2021-08-27 15:56:23,088 INFO SimpleSubprocess MakeCool - 0:01:19 2021-08-27 15:56:23,088 DEBUG SimpleSubprocess cp "/tmp/tmpq0n8z0j5/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-27 15:56:23,109 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:56:23,112 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt 2021-08-27 15:56:23,112 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-27 15:56:23,112 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 15:56:23,112 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 15:56:23,112 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-27 15:56:23,136 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":50000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt" "/tmp/tmpagifqvtr/inter_no_balanced.cool" 2021-08-27 15:57:39,031 INFO SimpleSubprocess MakeCool - 0:01:15 2021-08-27 15:57:39,032 DEBUG SimpleSubprocess cp "/tmp/tmpagifqvtr/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-27 15:57:39,050 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:57:39,085 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-27 15:57:39,085 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_5kb.cool 2021-08-27 15:57:39,085 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 15:57:39,114 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpyfgnkvat/inter.cool" 2021-08-27 15:57:39,146 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 15:57:39,146 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpyfgnkvat/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 15:57:44,912 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-08-27 15:57:44,912 DEBUG SimpleSubprocess cp "/tmp/tmpyfgnkvat/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_5kb.cool" 2021-08-27 15:57:44,943 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:57:44,976 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-27 15:57:44,976 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_10kb.cool 2021-08-27 15:57:44,976 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 15:57:44,976 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp4tbkndnj/inter.cool" 2021-08-27 15:57:45,001 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 15:57:45,001 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp4tbkndnj/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 15:57:48,014 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-27 15:57:48,015 DEBUG SimpleSubprocess cp "/tmp/tmp4tbkndnj/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_10kb.cool" 2021-08-27 15:57:48,040 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:57:48,043 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-27 15:57:48,043 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_20kb.cool 2021-08-27 15:57:48,043 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 15:57:48,044 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmplfre7g4y/inter.cool" 2021-08-27 15:57:48,066 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 15:57:48,066 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmplfre7g4y/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 15:57:50,216 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-27 15:57:50,217 DEBUG SimpleSubprocess cp "/tmp/tmplfre7g4y/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_20kb.cool" 2021-08-27 15:57:50,241 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:57:50,244 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-27 15:57:50,244 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_25kb.cool 2021-08-27 15:57:50,244 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 15:57:50,296 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmps7ki6cu9/inter.cool" 2021-08-27 15:57:50,319 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 15:57:50,319 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmps7ki6cu9/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 15:57:52,274 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-27 15:57:52,274 DEBUG SimpleSubprocess cp "/tmp/tmps7ki6cu9/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_25kb.cool" 2021-08-27 15:57:52,295 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:57:52,298 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-27 15:57:52,298 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_50kb.cool 2021-08-27 15:57:52,298 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 15:57:52,299 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpw3fkwq98/inter.cool" 2021-08-27 15:57:52,316 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 15:57:52,316 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpw3fkwq98/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 15:57:53,574 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-27 15:57:53,575 DEBUG SimpleSubprocess cp "/tmp/tmpw3fkwq98/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_50kb.cool" 2021-08-27 15:57:53,592 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:57:53,596 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt 2021-08-27 15:57:53,602 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-27 15:57:53,603 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_5kb.cool 2021-08-27 15:57:53,603 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt 2021-08-27 15:57:53,603 INFO AddWeight Chromosome: chr11 2021-08-27 15:57:53,603 INFO AddWeight Resolution [bp]: 5000 2021-08-27 15:57:53,729 INFO AddWeight AddWeight successfully finished 2021-08-27 15:57:53,730 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_10kb.cool 2021-08-27 15:57:53,730 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt 2021-08-27 15:57:53,730 INFO AddWeight Chromosome: chr11 2021-08-27 15:57:53,730 INFO AddWeight Resolution [bp]: 10000 2021-08-27 15:57:53,778 INFO AddWeight AddWeight successfully finished 2021-08-27 15:57:53,778 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_20kb.cool 2021-08-27 15:57:53,778 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt 2021-08-27 15:57:53,778 INFO AddWeight Chromosome: chr11 2021-08-27 15:57:53,778 INFO AddWeight Resolution [bp]: 20000 2021-08-27 15:57:53,809 INFO AddWeight AddWeight successfully finished 2021-08-27 15:57:53,809 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_25kb.cool 2021-08-27 15:57:53,810 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt 2021-08-27 15:57:53,810 INFO AddWeight Chromosome: chr11 2021-08-27 15:57:53,810 INFO AddWeight Resolution [bp]: 25000 2021-08-27 15:57:53,837 INFO AddWeight AddWeight successfully finished 2021-08-27 15:57:53,837 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_50kb.cool 2021-08-27 15:57:53,837 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt 2021-08-27 15:57:53,837 INFO AddWeight Chromosome: chr11 2021-08-27 15:57:53,837 INFO AddWeight Resolution [bp]: 50000 2021-08-27 15:57:53,858 INFO AddWeight AddWeight successfully finished 2021-08-27 15:57:53,860 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.hic 2021-08-27 15:57:53,860 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_norm.hic 2021-08-27 15:57:53,860 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt 2021-08-27 15:57:53,860 INFO Vector2HiC Threads: 10 2021-08-27 15:57:53,880 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.hic" "/tmp/tmp5k6mjm3f/inter.hic" 2021-08-27 15:57:54,179 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 15:57:54,180 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-08-27 15:57:54,181 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5k6mjm3f/inter.hic" "/tmp/tmp5k6mjm3f/vector.txt" 2021-08-27 15:57:58,784 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-27 15:57:58,784 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-08-27 15:57:58,785 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5k6mjm3f/inter.hic" "/tmp/tmp5k6mjm3f/vector.txt" 2021-08-27 15:58:02,727 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-27 15:58:02,728 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-08-27 15:58:02,728 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5k6mjm3f/inter.hic" "/tmp/tmp5k6mjm3f/vector.txt" 2021-08-27 15:58:06,546 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-27 15:58:06,546 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-08-27 15:58:06,546 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5k6mjm3f/inter.hic" "/tmp/tmp5k6mjm3f/vector.txt" 2021-08-27 15:58:10,442 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-27 15:58:10,443 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-08-27 15:58:10,443 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5k6mjm3f/inter.hic" "/tmp/tmp5k6mjm3f/vector.txt" 2021-08-27 15:58:14,366 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-27 15:58:14,367 DEBUG SimpleSubprocess cp "/tmp/tmp5k6mjm3f/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_norm.hic" 2021-08-27 15:58:14,776 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 15:58:14,837 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/merged_nodups.txt" 2021-08-27 16:00:13,851 INFO SimpleSubprocess CopyResult - 0:01:59 2021-08-27 16:00:13,886 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter.pairs.txt" 2021-08-27 16:00:28,907 INFO SimpleSubprocess CopyResult - 0:00:15 2021-08-27 16:00:28,907 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/vector.txt" 2021-08-27 16:00:29,039 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:29,040 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter.hic" 2021-08-27 16:00:33,017 INFO SimpleSubprocess CopyResult - 0:00:03 2021-08-27 16:00:33,027 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_statistics.txt" 2021-08-27 16:00:33,050 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:33,050 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_no_balanced_5kb.cool" 2021-08-27 16:00:33,279 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:33,280 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_5kb.cool" 2021-08-27 16:00:33,639 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:33,640 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_no_balanced_10kb.cool" 2021-08-27 16:00:33,826 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:33,826 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_10kb.cool" 2021-08-27 16:00:34,029 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:34,029 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_no_balanced_20kb.cool" 2021-08-27 16:00:34,144 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:34,144 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_20kb.cool" 2021-08-27 16:00:34,369 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:34,369 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_no_balanced_25kb.cool" 2021-08-27 16:00:34,499 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:34,500 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_25kb.cool" 2021-08-27 16:00:34,624 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:34,624 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_no_balanced_50kb.cool" 2021-08-27 16:00:34,830 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:34,830 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/inter_50kb.cool" 2021-08-27 16:00:34,927 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 16:00:35,193 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__" 2021-08-27 16:01:06,374 INFO SimpleSubprocess RemoveTemp - 0:00:31 2021-08-27 16:01:06,375 INFO BenchmarkPipeline 'SRR3179589' FINISHED, SUMMARY TIME - 13:15:29 2021-09-01 12:23:13,265 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179589' --- 2021-09-01 12:23:13,284 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__" 2021-09-01 12:23:13,293 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,293 INFO BenchmarkPipeline 'SRR3179589' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,782 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179589' --- 2021-09-02 13:38:17,782 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179589/__temp__" 2021-09-02 13:38:17,790 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,791 INFO BenchmarkPipeline 'SRR3179589' FINISHED, SUMMARY TIME - 0:00:00