2021-09-29 15:42:08,129 INFO BenchmarkPipeline --- START PROCESSING 'SRR8453405' --- 2021-09-29 15:42:08,129 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453405.sra 2021-09-29 15:42:08,129 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__ 2021-09-29 15:42:08,184 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpsj8uk98b "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453405.sra" 2021-09-29 16:21:24,684 INFO SimpleSubprocess Sra2FastQ - 0:39:16 2021-09-29 16:21:24,700 DEBUG SimpleSubprocess gzip /tmp/tmpsj8uk98b/* 2021-09-29 17:50:15,444 INFO SimpleSubprocess GZipFastQ - 1:28:50 2021-09-29 17:50:15,458 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/fastq"; mv /tmp/tmpsj8uk98b/SRR8453405_2.fastq.gz /tmp/tmpsj8uk98b/SRR8453405_R2.fastq.gz; mv /tmp/tmpsj8uk98b/SRR8453405_1.fastq.gz /tmp/tmpsj8uk98b/SRR8453405_R1.fastq.gz; cp /tmp/tmpsj8uk98b/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/fastq" 2021-09-29 17:52:21,812 INFO SimpleSubprocess CopyFiles - 0:02:06 2021-09-29 17:52:23,201 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__ 2021-09-29 17:52:23,201 INFO Juicer Genome assembly: mm10 2021-09-29 17:52:23,201 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-29 17:52:23,201 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 17:52:23,201 INFO Juicer Enzyme: DpnII 2021-09-29 17:52:23,201 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-29 17:52:23,202 INFO Juicer Threads: 10 2021-09-29 17:52:23,202 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/HIC_tmp" 2021-09-29 17:52:23,210 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-29 17:52:23,211 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/SRR8453405/__temp__" 2021-09-30 03:19:53,446 INFO SimpleSubprocess Juicer - 9:27:30 2021-09-30 03:19:53,465 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/SRR8453405/__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/SRR8453405/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/splits/SRR8453405_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/splits/SRR8453405_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/splits/SRR8453405.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/splits/SRR8453405.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 [2021-09-30T01:58:27,904] [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 [2021-09-30T02:45:04,058] [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/SRR8453405/__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 [2021-09-30T03:19:53,029] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__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/SRR8453405/__temp__/aligned for results 2021-09-30 03:19:53,526 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/merged_nodups.txt 2021-09-30 03:19:53,527 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt 2021-09-30 03:19:53,527 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp7ougwhx3/inter.pairs.txt" 2021-09-30 03:21:22,706 INFO SimpleSubprocess MakeInterPairs - 0:01:29 2021-09-30 03:21:22,707 DEBUG SimpleSubprocess cp "/tmp/tmp7ougwhx3/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt" 2021-09-30 03:21:25,147 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-30 03:21:26,507 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt 2021-09-30 03:21:26,508 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-30 03:21:26,508 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 03:21:26,508 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 03:21:26,508 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-30 03:21:26,558 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/SRR8453405/__temp__/aligned/inter.pairs.txt" "/tmp/tmptnm5g765/inter_no_balanced.cool" 2021-09-30 03:23:55,227 INFO SimpleSubprocess MakeCool - 0:02:28 2021-09-30 03:23:55,227 DEBUG SimpleSubprocess cp "/tmp/tmptnm5g765/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-30 03:23:55,277 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:23:55,284 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt 2021-09-30 03:23:55,284 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-30 03:23:55,284 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 03:23:55,284 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 03:23:55,284 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-30 03:23:55,284 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/SRR8453405/__temp__/aligned/inter.pairs.txt" "/tmp/tmp96av5bi8/inter_no_balanced.cool" 2021-09-30 03:26:05,322 INFO SimpleSubprocess MakeCool - 0:02:10 2021-09-30 03:26:05,323 DEBUG SimpleSubprocess cp "/tmp/tmp96av5bi8/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-30 03:26:05,362 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:26:05,425 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt 2021-09-30 03:26:05,425 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-30 03:26:05,425 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 03:26:05,425 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 03:26:05,425 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-30 03:26:05,426 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/SRR8453405/__temp__/aligned/inter.pairs.txt" "/tmp/tmp0rn2wsev/inter_no_balanced.cool" 2021-09-30 03:28:09,587 INFO SimpleSubprocess MakeCool - 0:02:04 2021-09-30 03:28:09,587 DEBUG SimpleSubprocess cp "/tmp/tmp0rn2wsev/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-30 03:28:09,624 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:28:09,628 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt 2021-09-30 03:28:09,628 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-30 03:28:09,628 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 03:28:09,628 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 03:28:09,628 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-30 03:28:09,660 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/SRR8453405/__temp__/aligned/inter.pairs.txt" "/tmp/tmp39lbmc0a/inter_no_balanced.cool" 2021-09-30 03:30:11,044 INFO SimpleSubprocess MakeCool - 0:02:01 2021-09-30 03:30:11,044 DEBUG SimpleSubprocess cp "/tmp/tmp39lbmc0a/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-30 03:30:11,078 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:30:11,083 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt 2021-09-30 03:30:11,083 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-30 03:30:11,083 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 03:30:11,083 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 03:30:11,083 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-30 03:30:11,083 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/SRR8453405/__temp__/aligned/inter.pairs.txt" "/tmp/tmpka1mezjx/inter_no_balanced.cool" 2021-09-30 03:32:04,768 INFO SimpleSubprocess MakeCool - 0:01:53 2021-09-30 03:32:04,769 DEBUG SimpleSubprocess cp "/tmp/tmpka1mezjx/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-30 03:32:04,795 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:32:04,800 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-30 03:32:04,800 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_5kb.cool 2021-09-30 03:32:04,800 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-30 03:32:04,839 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp2fc8jfrj/inter.cool" 2021-09-30 03:32:04,889 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 03:32:04,890 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp2fc8jfrj/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-30 03:32:11,195 INFO SimpleSubprocess NormalizeCool - 0:00:06 2021-09-30 03:32:11,195 DEBUG SimpleSubprocess cp "/tmp/tmp2fc8jfrj/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_5kb.cool" 2021-09-30 03:32:11,244 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:32:11,251 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-30 03:32:11,251 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_10kb.cool 2021-09-30 03:32:11,251 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-30 03:32:11,251 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpsbwc72dn/inter.cool" 2021-09-30 03:32:11,291 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 03:32:11,292 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpsbwc72dn/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-30 03:32:14,542 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-30 03:32:14,542 DEBUG SimpleSubprocess cp "/tmp/tmpsbwc72dn/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_10kb.cool" 2021-09-30 03:32:14,583 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:32:14,589 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-30 03:32:14,589 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_20kb.cool 2021-09-30 03:32:14,589 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-30 03:32:14,589 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpbr2659de/inter.cool" 2021-09-30 03:32:14,625 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 03:32:14,625 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpbr2659de/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-30 03:32:16,881 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-30 03:32:16,881 DEBUG SimpleSubprocess cp "/tmp/tmpbr2659de/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_20kb.cool" 2021-09-30 03:32:16,936 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:32:16,941 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-30 03:32:16,941 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_25kb.cool 2021-09-30 03:32:16,941 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-30 03:32:16,942 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpxd_2vdn_/inter.cool" 2021-09-30 03:32:16,975 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 03:32:16,975 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpxd_2vdn_/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-30 03:32:18,975 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-30 03:32:18,975 DEBUG SimpleSubprocess cp "/tmp/tmpxd_2vdn_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_25kb.cool" 2021-09-30 03:32:19,009 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:32:19,014 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-30 03:32:19,014 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_50kb.cool 2021-09-30 03:32:19,014 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-30 03:32:19,014 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmppigemxjv/inter.cool" 2021-09-30 03:32:19,041 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 03:32:19,041 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmppigemxjv/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-30 03:32:20,418 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-30 03:32:20,419 DEBUG SimpleSubprocess cp "/tmp/tmppigemxjv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_50kb.cool" 2021-09-30 03:32:20,446 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:32:20,512 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt 2021-09-30 03:32:20,519 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-30 03:32:20,520 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_5kb.cool 2021-09-30 03:32:20,520 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt 2021-09-30 03:32:20,520 INFO AddWeight Chromosome: chr11 2021-09-30 03:32:20,520 INFO AddWeight Resolution [bp]: 5000 2021-09-30 03:32:20,605 INFO AddWeight AddWeight successfully finished 2021-09-30 03:32:20,605 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_10kb.cool 2021-09-30 03:32:20,605 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt 2021-09-30 03:32:20,605 INFO AddWeight Chromosome: chr11 2021-09-30 03:32:20,606 INFO AddWeight Resolution [bp]: 10000 2021-09-30 03:32:20,653 INFO AddWeight AddWeight successfully finished 2021-09-30 03:32:20,653 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_20kb.cool 2021-09-30 03:32:20,653 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt 2021-09-30 03:32:20,653 INFO AddWeight Chromosome: chr11 2021-09-30 03:32:20,653 INFO AddWeight Resolution [bp]: 20000 2021-09-30 03:32:20,684 INFO AddWeight AddWeight successfully finished 2021-09-30 03:32:20,684 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_25kb.cool 2021-09-30 03:32:20,684 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt 2021-09-30 03:32:20,684 INFO AddWeight Chromosome: chr11 2021-09-30 03:32:20,684 INFO AddWeight Resolution [bp]: 25000 2021-09-30 03:32:20,711 INFO AddWeight AddWeight successfully finished 2021-09-30 03:32:20,711 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_50kb.cool 2021-09-30 03:32:20,711 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt 2021-09-30 03:32:20,711 INFO AddWeight Chromosome: chr11 2021-09-30 03:32:20,711 INFO AddWeight Resolution [bp]: 50000 2021-09-30 03:32:20,731 INFO AddWeight AddWeight successfully finished 2021-09-30 03:32:20,763 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.hic 2021-09-30 03:32:20,763 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_norm.hic 2021-09-30 03:32:20,763 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt 2021-09-30 03:32:20,763 INFO Vector2HiC Threads: 10 2021-09-30 03:32:20,804 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.hic" "/tmp/tmpe3d59lru/inter.hic" 2021-09-30 03:32:21,167 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 03:32:21,167 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-09-30 03:32:21,169 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpe3d59lru/inter.hic" "/tmp/tmpe3d59lru/vector.txt" 2021-09-30 03:32:25,886 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 03:32:25,886 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-09-30 03:32:25,887 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpe3d59lru/inter.hic" "/tmp/tmpe3d59lru/vector.txt" 2021-09-30 03:32:29,959 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 03:32:29,960 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-09-30 03:32:29,960 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpe3d59lru/inter.hic" "/tmp/tmpe3d59lru/vector.txt" 2021-09-30 03:32:34,728 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 03:32:34,728 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-09-30 03:32:34,823 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpe3d59lru/inter.hic" "/tmp/tmpe3d59lru/vector.txt" 2021-09-30 03:32:38,522 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-30 03:32:38,522 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-09-30 03:32:38,522 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpe3d59lru/inter.hic" "/tmp/tmpe3d59lru/vector.txt" 2021-09-30 03:32:42,207 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-30 03:32:42,208 DEBUG SimpleSubprocess cp "/tmp/tmpe3d59lru/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_norm.hic" 2021-09-30 03:32:42,640 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 03:32:42,706 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/merged_nodups.txt" 2021-09-30 03:34:09,275 INFO SimpleSubprocess CopyResult - 0:01:26 2021-09-30 03:34:09,275 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter.pairs.txt" 2021-09-30 03:34:30,379 INFO SimpleSubprocess CopyResult - 0:00:21 2021-09-30 03:34:30,379 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/vector.txt" 2021-09-30 03:34:30,442 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:30,442 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter.hic" 2021-09-30 03:34:33,663 INFO SimpleSubprocess CopyResult - 0:00:03 2021-09-30 03:34:33,663 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_statistics.txt" 2021-09-30 03:34:33,672 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:33,672 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_no_balanced_5kb.cool" 2021-09-30 03:34:34,099 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:34,100 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_5kb.cool" 2021-09-30 03:34:34,483 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:34,483 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_no_balanced_10kb.cool" 2021-09-30 03:34:34,711 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:34,711 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_10kb.cool" 2021-09-30 03:34:34,900 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:34,900 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_no_balanced_20kb.cool" 2021-09-30 03:34:35,225 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:35,255 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_20kb.cool" 2021-09-30 03:34:35,423 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:35,423 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_no_balanced_25kb.cool" 2021-09-30 03:34:35,575 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:35,576 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_25kb.cool" 2021-09-30 03:34:35,824 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:35,824 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_no_balanced_50kb.cool" 2021-09-30 03:34:35,964 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:35,964 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/inter_50kb.cool" 2021-09-30 03:34:36,083 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 03:34:36,141 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453405/__temp__" 2021-09-30 03:34:49,177 INFO SimpleSubprocess RemoveTemp - 0:00:13 2021-09-30 03:34:49,177 INFO BenchmarkPipeline 'SRR8453405' FINISHED, SUMMARY TIME - 11:52:41