2021-09-23 21:20:58,443 INFO BenchmarkPipeline --- START PROCESSING 'SRR8284495-SRR8284496' --- 2021-09-23 21:20:58,443 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284495.sra 2021-09-23 21:20:58,443 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__ 2021-09-23 21:20:58,474 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpel9eessp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284495.sra" 2021-09-23 21:53:43,282 INFO SimpleSubprocess Sra2FastQ - 0:32:44 2021-09-23 21:53:43,327 DEBUG SimpleSubprocess gzip /tmp/tmpel9eessp/* 2021-09-23 23:08:10,390 INFO SimpleSubprocess GZipFastQ - 1:14:27 2021-09-23 23:08:10,442 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/fastq"; mv /tmp/tmpel9eessp/SRR8284495_1.fastq.gz /tmp/tmpel9eessp/SRR8284495_R1.fastq.gz; mv /tmp/tmpel9eessp/SRR8284495_2.fastq.gz /tmp/tmpel9eessp/SRR8284495_R2.fastq.gz; cp /tmp/tmpel9eessp/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/fastq" 2021-09-23 23:09:10,091 INFO SimpleSubprocess CopyFiles - 0:00:59 2021-09-23 23:09:11,857 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284496.sra 2021-09-23 23:09:11,857 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__ 2021-09-23 23:09:11,858 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpqetmdcda "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284496.sra" 2021-09-23 23:17:36,630 INFO SimpleSubprocess Sra2FastQ - 0:08:24 2021-09-23 23:17:36,631 DEBUG SimpleSubprocess gzip /tmp/tmpqetmdcda/* 2021-09-23 23:42:17,797 INFO SimpleSubprocess GZipFastQ - 0:24:41 2021-09-23 23:42:17,817 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/fastq"; mv /tmp/tmpqetmdcda/SRR8284496_1.fastq.gz /tmp/tmpqetmdcda/SRR8284496_R1.fastq.gz; mv /tmp/tmpqetmdcda/SRR8284496_2.fastq.gz /tmp/tmpqetmdcda/SRR8284496_R2.fastq.gz; cp /tmp/tmpqetmdcda/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/fastq" 2021-09-23 23:42:22,131 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-23 23:42:22,941 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__ 2021-09-23 23:42:22,941 INFO Juicer Genome assembly: mm10 2021-09-23 23:42:22,941 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-23 23:42:22,941 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 23:42:22,941 INFO Juicer Enzyme: DpnII 2021-09-23 23:42:22,941 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-23 23:42:22,941 INFO Juicer Threads: 10 2021-09-23 23:42:22,941 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/HIC_tmp" 2021-09-23 23:42:22,981 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-23 23:42:22,981 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/SRR8284495-SRR8284496/__temp__" 2021-09-24 10:46:32,732 INFO SimpleSubprocess Juicer - 11:04:09 2021-09-24 10:46:32,763 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/SRR8284495-SRR8284496/__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/SRR8284495-SRR8284496/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284495_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284495_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284495.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284495.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284496_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284496_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284496.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/splits/SRR8284496.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 [2021-09-24T09:28:38,226] [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 [2021-09-24T10:12:19,728] [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/SRR8284495-SRR8284496/__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 [2021-09-24T10:46:32,196] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__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/SRR8284495-SRR8284496/__temp__/aligned for results 2021-09-24 10:46:32,820 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/merged_nodups.txt 2021-09-24 10:46:32,820 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt 2021-09-24 10:46:32,871 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpu_82l57s/inter.pairs.txt" 2021-09-24 10:48:26,348 INFO SimpleSubprocess MakeInterPairs - 0:01:53 2021-09-24 10:48:26,349 DEBUG SimpleSubprocess cp "/tmp/tmpu_82l57s/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt" 2021-09-24 10:48:29,220 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-24 10:48:30,413 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt 2021-09-24 10:48:30,413 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-24 10:48:30,413 INFO Pairs2Cool Genome assembly: mm10 2021-09-24 10:48:30,413 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-24 10:48:30,413 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-24 10:48:30,413 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/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt" "/tmp/tmp4k4htb33/inter_no_balanced.cool" 2021-09-24 10:51:36,979 INFO SimpleSubprocess MakeCool - 0:03:06 2021-09-24 10:51:36,980 DEBUG SimpleSubprocess cp "/tmp/tmp4k4htb33/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-24 10:51:37,057 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 10:51:37,066 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt 2021-09-24 10:51:37,066 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-24 10:51:37,066 INFO Pairs2Cool Genome assembly: mm10 2021-09-24 10:51:37,066 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-24 10:51:37,066 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-24 10:51:37,067 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/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2sy9rvqs/inter_no_balanced.cool" 2021-09-24 10:54:20,322 INFO SimpleSubprocess MakeCool - 0:02:43 2021-09-24 10:54:20,323 DEBUG SimpleSubprocess cp "/tmp/tmp2sy9rvqs/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-24 10:54:20,382 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 10:54:20,390 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt 2021-09-24 10:54:20,390 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-24 10:54:20,390 INFO Pairs2Cool Genome assembly: mm10 2021-09-24 10:54:20,390 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-24 10:54:20,390 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-24 10:54:20,390 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/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt" "/tmp/tmpj3sf8nlh/inter_no_balanced.cool" 2021-09-24 10:56:57,480 INFO SimpleSubprocess MakeCool - 0:02:37 2021-09-24 10:56:57,480 DEBUG SimpleSubprocess cp "/tmp/tmpj3sf8nlh/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-24 10:56:57,534 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 10:56:57,541 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt 2021-09-24 10:56:57,541 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-24 10:56:57,541 INFO Pairs2Cool Genome assembly: mm10 2021-09-24 10:56:57,541 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-24 10:56:57,541 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-24 10:56:57,541 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/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt" "/tmp/tmprz4q5gsh/inter_no_balanced.cool" 2021-09-24 10:59:30,049 INFO SimpleSubprocess MakeCool - 0:02:32 2021-09-24 10:59:30,050 DEBUG SimpleSubprocess cp "/tmp/tmprz4q5gsh/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-24 10:59:30,103 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 10:59:30,109 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt 2021-09-24 10:59:30,109 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-24 10:59:30,109 INFO Pairs2Cool Genome assembly: mm10 2021-09-24 10:59:30,110 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-24 10:59:30,110 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-24 10:59:30,110 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/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt" "/tmp/tmpw95gjn0l/inter_no_balanced.cool" 2021-09-24 11:01:57,357 INFO SimpleSubprocess MakeCool - 0:02:27 2021-09-24 11:01:57,357 DEBUG SimpleSubprocess cp "/tmp/tmpw95gjn0l/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-24 11:01:57,399 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 11:01:57,406 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-24 11:01:57,406 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_5kb.cool 2021-09-24 11:01:57,406 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-24 11:01:57,407 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp129br1g5/inter.cool" 2021-09-24 11:01:57,473 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-24 11:01:57,473 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp129br1g5/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-24 11:02:10,931 INFO SimpleSubprocess NormalizeCool - 0:00:13 2021-09-24 11:02:10,931 DEBUG SimpleSubprocess cp "/tmp/tmp129br1g5/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_5kb.cool" 2021-09-24 11:02:10,998 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 11:02:11,023 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-24 11:02:11,023 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_10kb.cool 2021-09-24 11:02:11,023 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-24 11:02:11,024 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpldmlu00f/inter.cool" 2021-09-24 11:02:11,082 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-24 11:02:11,082 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpldmlu00f/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-24 11:02:20,424 INFO SimpleSubprocess NormalizeCool - 0:00:09 2021-09-24 11:02:20,424 DEBUG SimpleSubprocess cp "/tmp/tmpldmlu00f/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_10kb.cool" 2021-09-24 11:02:20,484 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 11:02:20,492 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-24 11:02:20,492 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_20kb.cool 2021-09-24 11:02:20,492 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-24 11:02:20,521 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpyvjeo36k/inter.cool" 2021-09-24 11:02:20,574 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-24 11:02:20,574 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpyvjeo36k/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-24 11:02:26,932 INFO SimpleSubprocess NormalizeCool - 0:00:06 2021-09-24 11:02:26,932 DEBUG SimpleSubprocess cp "/tmp/tmpyvjeo36k/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_20kb.cool" 2021-09-24 11:02:26,985 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 11:02:26,993 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-24 11:02:26,993 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_25kb.cool 2021-09-24 11:02:26,993 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-24 11:02:26,993 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp1h5ofeny/inter.cool" 2021-09-24 11:02:27,043 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-24 11:02:27,043 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp1h5ofeny/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-24 11:02:32,951 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-24 11:02:32,952 DEBUG SimpleSubprocess cp "/tmp/tmp1h5ofeny/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_25kb.cool" 2021-09-24 11:02:33,005 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 11:02:33,012 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-24 11:02:33,012 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_50kb.cool 2021-09-24 11:02:33,012 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-24 11:02:33,012 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpvgkpswld/inter.cool" 2021-09-24 11:02:33,057 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-24 11:02:33,057 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpvgkpswld/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-24 11:02:36,440 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-24 11:02:36,440 DEBUG SimpleSubprocess cp "/tmp/tmpvgkpswld/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_50kb.cool" 2021-09-24 11:02:36,481 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 11:02:36,488 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt 2021-09-24 11:02:36,496 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-24 11:02:36,496 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_5kb.cool 2021-09-24 11:02:36,496 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt 2021-09-24 11:02:36,496 INFO AddWeight Chromosome: chr5 2021-09-24 11:02:36,496 INFO AddWeight Resolution [bp]: 5000 2021-09-24 11:02:36,566 INFO AddWeight AddWeight successfully finished 2021-09-24 11:02:36,566 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_10kb.cool 2021-09-24 11:02:36,566 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt 2021-09-24 11:02:36,566 INFO AddWeight Chromosome: chr5 2021-09-24 11:02:36,566 INFO AddWeight Resolution [bp]: 10000 2021-09-24 11:02:36,606 INFO AddWeight AddWeight successfully finished 2021-09-24 11:02:36,606 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_20kb.cool 2021-09-24 11:02:36,606 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt 2021-09-24 11:02:36,606 INFO AddWeight Chromosome: chr5 2021-09-24 11:02:36,606 INFO AddWeight Resolution [bp]: 20000 2021-09-24 11:02:36,633 INFO AddWeight AddWeight successfully finished 2021-09-24 11:02:36,633 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_25kb.cool 2021-09-24 11:02:36,633 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt 2021-09-24 11:02:36,633 INFO AddWeight Chromosome: chr5 2021-09-24 11:02:36,634 INFO AddWeight Resolution [bp]: 25000 2021-09-24 11:02:36,658 INFO AddWeight AddWeight successfully finished 2021-09-24 11:02:36,658 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_50kb.cool 2021-09-24 11:02:36,658 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt 2021-09-24 11:02:36,658 INFO AddWeight Chromosome: chr5 2021-09-24 11:02:36,658 INFO AddWeight Resolution [bp]: 50000 2021-09-24 11:02:36,677 INFO AddWeight AddWeight successfully finished 2021-09-24 11:02:36,679 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.hic 2021-09-24 11:02:36,679 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_norm.hic 2021-09-24 11:02:36,679 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt 2021-09-24 11:02:36,679 INFO Vector2HiC Threads: 10 2021-09-24 11:02:36,701 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.hic" "/tmp/tmpr1joffag/inter.hic" 2021-09-24 11:02:37,107 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-24 11:02:37,107 INFO Vector2HiC Vector: vector c-tale_normalization chr5 5000 BP 2021-09-24 11:02:37,108 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpr1joffag/inter.hic" "/tmp/tmpr1joffag/vector.txt" 2021-09-24 11:02:41,828 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-24 11:02:41,829 INFO Vector2HiC Vector: vector c-tale_normalization chr5 10000 BP 2021-09-24 11:02:41,829 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpr1joffag/inter.hic" "/tmp/tmpr1joffag/vector.txt" 2021-09-24 11:02:45,817 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-24 11:02:45,817 INFO Vector2HiC Vector: vector c-tale_normalization chr5 20000 BP 2021-09-24 11:02:45,837 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpr1joffag/inter.hic" "/tmp/tmpr1joffag/vector.txt" 2021-09-24 11:02:49,702 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-24 11:02:49,702 INFO Vector2HiC Vector: vector c-tale_normalization chr5 25000 BP 2021-09-24 11:02:49,702 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpr1joffag/inter.hic" "/tmp/tmpr1joffag/vector.txt" 2021-09-24 11:02:53,659 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-24 11:02:53,659 INFO Vector2HiC Vector: vector c-tale_normalization chr5 50000 BP 2021-09-24 11:02:53,660 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpr1joffag/inter.hic" "/tmp/tmpr1joffag/vector.txt" 2021-09-24 11:02:57,605 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-24 11:02:57,605 DEBUG SimpleSubprocess cp "/tmp/tmpr1joffag/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_norm.hic" 2021-09-24 11:02:58,082 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-24 11:02:58,157 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/merged_nodups.txt" 2021-09-24 11:04:59,863 INFO SimpleSubprocess CopyResult - 0:02:01 2021-09-24 11:04:59,892 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter.pairs.txt" 2021-09-24 11:05:23,616 INFO SimpleSubprocess CopyResult - 0:00:23 2021-09-24 11:05:23,616 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/vector.txt" 2021-09-24 11:05:23,715 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:23,715 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter.hic" 2021-09-24 11:05:28,521 INFO SimpleSubprocess CopyResult - 0:00:04 2021-09-24 11:05:28,521 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_statistics.txt" 2021-09-24 11:05:28,529 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:28,529 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_no_balanced_5kb.cool" 2021-09-24 11:05:29,385 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:29,385 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_5kb.cool" 2021-09-24 11:05:30,391 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-24 11:05:30,391 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_no_balanced_10kb.cool" 2021-09-24 11:05:30,972 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:30,972 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_10kb.cool" 2021-09-24 11:05:31,518 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:31,518 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_no_balanced_20kb.cool" 2021-09-24 11:05:32,277 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:32,277 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_20kb.cool" 2021-09-24 11:05:32,943 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:32,944 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_no_balanced_25kb.cool" 2021-09-24 11:05:33,432 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:33,433 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_25kb.cool" 2021-09-24 11:05:34,200 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:34,201 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_no_balanced_50kb.cool" 2021-09-24 11:05:34,591 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:34,592 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/inter_50kb.cool" 2021-09-24 11:05:34,975 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-24 11:05:35,239 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284495-SRR8284496/__temp__" 2021-09-24 11:05:59,590 INFO SimpleSubprocess RemoveTemp - 0:00:24 2021-09-24 11:05:59,590 INFO BenchmarkPipeline 'SRR8284495-SRR8284496' FINISHED, SUMMARY TIME - 13:45:01