2021-09-23 13:18:26,224 INFO BenchmarkPipeline --- START PROCESSING 'SRR7500320' --- 2021-09-23 13:18:26,224 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500320.sra 2021-09-23 13:18:26,224 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__ 2021-09-23 13:18:26,224 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpxg2cvmd5 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500320.sra" 2021-09-23 13:36:06,203 INFO SimpleSubprocess Sra2FastQ - 0:17:39 2021-09-23 13:36:06,215 DEBUG SimpleSubprocess gzip /tmp/tmpxg2cvmd5/* 2021-09-23 14:15:38,601 INFO SimpleSubprocess GZipFastQ - 0:39:32 2021-09-23 14:15:38,602 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/fastq"; mv /tmp/tmpxg2cvmd5/SRR7500320_1.fastq.gz /tmp/tmpxg2cvmd5/SRR7500320_R1.fastq.gz; mv /tmp/tmpxg2cvmd5/SRR7500320_2.fastq.gz /tmp/tmpxg2cvmd5/SRR7500320_R2.fastq.gz; cp /tmp/tmpxg2cvmd5/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/fastq" 2021-09-23 14:15:46,099 INFO SimpleSubprocess CopyFiles - 0:00:07 2021-09-23 14:15:47,345 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__ 2021-09-23 14:15:47,346 INFO Juicer Genome assembly: mm10 2021-09-23 14:15:47,346 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-23 14:15:47,346 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 14:15:47,346 INFO Juicer Enzyme: DpnII 2021-09-23 14:15:47,346 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-23 14:15:47,346 INFO Juicer Threads: 10 2021-09-23 14:15:47,346 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/HIC_tmp" 2021-09-23 14:15:47,354 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-23 14:15:47,354 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/SRR7500320/__temp__" 2021-09-23 21:12:54,814 INFO SimpleSubprocess Juicer - 6:57:07 2021-09-23 21:12:54,844 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/SRR7500320/__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/SRR7500320/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/splits/SRR7500320_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/splits/SRR7500320_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/splits/SRR7500320.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/splits/SRR7500320.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 [2021-09-23T17:52:29,541] [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 [2021-09-23T19:23:15,693] [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/SRR7500320/__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 [2021-09-23T21:12:54,325] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__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/SRR7500320/__temp__/aligned for results 2021-09-23 21:12:54,870 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/merged_nodups.txt 2021-09-23 21:12:54,870 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt 2021-09-23 21:12:54,870 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/merged_nodups.txt" > "/tmp/tmptqa3d5xy/inter.pairs.txt" 2021-09-23 21:13:45,315 INFO SimpleSubprocess MakeInterPairs - 0:00:50 2021-09-23 21:13:45,315 DEBUG SimpleSubprocess cp "/tmp/tmptqa3d5xy/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt" 2021-09-23 21:13:46,653 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-23 21:13:46,842 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt 2021-09-23 21:13:46,842 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-23 21:13:46,843 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 21:13:46,843 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 21:13:46,843 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-23 21:13:46,898 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/SRR7500320/__temp__/aligned/inter.pairs.txt" "/tmp/tmpn8xzoxqc/inter_no_balanced.cool" 2021-09-23 21:15:06,634 INFO SimpleSubprocess MakeCool - 0:01:19 2021-09-23 21:15:06,634 DEBUG SimpleSubprocess cp "/tmp/tmpn8xzoxqc/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-23 21:15:06,664 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:15:06,698 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt 2021-09-23 21:15:06,698 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-23 21:15:06,698 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 21:15:06,698 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 21:15:06,698 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-23 21:15:06,698 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/SRR7500320/__temp__/aligned/inter.pairs.txt" "/tmp/tmpsylnooj5/inter_no_balanced.cool" 2021-09-23 21:16:16,719 INFO SimpleSubprocess MakeCool - 0:01:10 2021-09-23 21:16:16,719 DEBUG SimpleSubprocess cp "/tmp/tmpsylnooj5/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-23 21:16:16,743 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:16:16,746 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt 2021-09-23 21:16:16,746 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-23 21:16:16,746 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 21:16:16,746 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 21:16:16,746 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-23 21:16:16,746 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/SRR7500320/__temp__/aligned/inter.pairs.txt" "/tmp/tmpbjz8y89f/inter_no_balanced.cool" 2021-09-23 21:17:22,846 INFO SimpleSubprocess MakeCool - 0:01:06 2021-09-23 21:17:22,846 DEBUG SimpleSubprocess cp "/tmp/tmpbjz8y89f/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-23 21:17:22,869 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:17:22,872 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt 2021-09-23 21:17:22,872 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-23 21:17:22,873 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 21:17:22,873 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 21:17:22,873 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-23 21:17:22,873 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/SRR7500320/__temp__/aligned/inter.pairs.txt" "/tmp/tmpq_76w7zr/inter_no_balanced.cool" 2021-09-23 21:18:27,412 INFO SimpleSubprocess MakeCool - 0:01:04 2021-09-23 21:18:27,412 DEBUG SimpleSubprocess cp "/tmp/tmpq_76w7zr/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-23 21:18:27,434 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:18:27,436 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt 2021-09-23 21:18:27,436 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-23 21:18:27,437 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 21:18:27,437 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 21:18:27,437 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-23 21:18:27,437 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/SRR7500320/__temp__/aligned/inter.pairs.txt" "/tmp/tmpupi3i15v/inter_no_balanced.cool" 2021-09-23 21:19:30,580 INFO SimpleSubprocess MakeCool - 0:01:03 2021-09-23 21:19:30,580 DEBUG SimpleSubprocess cp "/tmp/tmpupi3i15v/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-23 21:19:30,600 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:19:30,604 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-23 21:19:30,604 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_5kb.cool 2021-09-23 21:19:30,604 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 21:19:30,618 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpf4qkszfz/inter.cool" 2021-09-23 21:19:30,649 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 21:19:30,649 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpf4qkszfz/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 21:19:37,758 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-23 21:19:37,758 DEBUG SimpleSubprocess cp "/tmp/tmpf4qkszfz/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_5kb.cool" 2021-09-23 21:19:37,787 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:19:37,791 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-23 21:19:37,791 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_10kb.cool 2021-09-23 21:19:37,791 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 21:19:37,810 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpg4f4fcwv/inter.cool" 2021-09-23 21:19:37,836 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 21:19:37,837 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpg4f4fcwv/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 21:19:41,655 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-23 21:19:41,655 DEBUG SimpleSubprocess cp "/tmp/tmpg4f4fcwv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_10kb.cool" 2021-09-23 21:19:41,681 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:19:41,882 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-23 21:19:41,882 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_20kb.cool 2021-09-23 21:19:41,882 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 21:19:41,882 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp215d4igm/inter.cool" 2021-09-23 21:19:41,907 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 21:19:41,907 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp215d4igm/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 21:19:44,631 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-23 21:19:44,631 DEBUG SimpleSubprocess cp "/tmp/tmp215d4igm/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_20kb.cool" 2021-09-23 21:19:44,655 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:19:44,658 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-23 21:19:44,658 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_25kb.cool 2021-09-23 21:19:44,658 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 21:19:44,659 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpn3iglmq6/inter.cool" 2021-09-23 21:19:44,681 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 21:19:44,681 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpn3iglmq6/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 21:19:47,166 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-23 21:19:47,166 DEBUG SimpleSubprocess cp "/tmp/tmpn3iglmq6/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_25kb.cool" 2021-09-23 21:19:47,187 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:19:47,189 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-23 21:19:47,189 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_50kb.cool 2021-09-23 21:19:47,189 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 21:19:47,209 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpr7hgwrdl/inter.cool" 2021-09-23 21:19:47,227 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 21:19:47,227 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpr7hgwrdl/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 21:19:48,992 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-23 21:19:48,993 DEBUG SimpleSubprocess cp "/tmp/tmpr7hgwrdl/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_50kb.cool" 2021-09-23 21:19:49,012 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:19:49,016 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt 2021-09-23 21:19:49,023 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-23 21:19:49,024 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_5kb.cool 2021-09-23 21:19:49,024 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt 2021-09-23 21:19:49,024 INFO AddWeight Chromosome: chr1 2021-09-23 21:19:49,024 INFO AddWeight Resolution [bp]: 5000 2021-09-23 21:19:49,146 INFO AddWeight AddWeight successfully finished 2021-09-23 21:19:49,147 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_10kb.cool 2021-09-23 21:19:49,147 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt 2021-09-23 21:19:49,147 INFO AddWeight Chromosome: chr1 2021-09-23 21:19:49,147 INFO AddWeight Resolution [bp]: 10000 2021-09-23 21:19:49,214 INFO AddWeight AddWeight successfully finished 2021-09-23 21:19:49,214 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_20kb.cool 2021-09-23 21:19:49,214 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt 2021-09-23 21:19:49,214 INFO AddWeight Chromosome: chr1 2021-09-23 21:19:49,214 INFO AddWeight Resolution [bp]: 20000 2021-09-23 21:19:49,255 INFO AddWeight AddWeight successfully finished 2021-09-23 21:19:49,255 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_25kb.cool 2021-09-23 21:19:49,255 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt 2021-09-23 21:19:49,255 INFO AddWeight Chromosome: chr1 2021-09-23 21:19:49,255 INFO AddWeight Resolution [bp]: 25000 2021-09-23 21:19:51,179 INFO AddWeight AddWeight successfully finished 2021-09-23 21:19:51,179 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_50kb.cool 2021-09-23 21:19:51,179 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt 2021-09-23 21:19:51,179 INFO AddWeight Chromosome: chr1 2021-09-23 21:19:51,179 INFO AddWeight Resolution [bp]: 50000 2021-09-23 21:19:51,205 INFO AddWeight AddWeight successfully finished 2021-09-23 21:19:51,207 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.hic 2021-09-23 21:19:51,207 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_norm.hic 2021-09-23 21:19:51,207 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt 2021-09-23 21:19:51,207 INFO Vector2HiC Threads: 10 2021-09-23 21:19:51,247 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.hic" "/tmp/tmp3zsc3sxl/inter.hic" 2021-09-23 21:19:51,525 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 21:19:51,525 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-09-23 21:19:51,527 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp3zsc3sxl/inter.hic" "/tmp/tmp3zsc3sxl/vector.txt" 2021-09-23 21:19:56,139 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-23 21:19:56,139 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-09-23 21:19:56,140 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp3zsc3sxl/inter.hic" "/tmp/tmp3zsc3sxl/vector.txt" 2021-09-23 21:20:00,593 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-23 21:20:00,594 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-09-23 21:20:00,595 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp3zsc3sxl/inter.hic" "/tmp/tmp3zsc3sxl/vector.txt" 2021-09-23 21:20:04,540 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 21:20:04,540 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-09-23 21:20:04,541 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp3zsc3sxl/inter.hic" "/tmp/tmp3zsc3sxl/vector.txt" 2021-09-23 21:20:08,538 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 21:20:08,538 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-09-23 21:20:08,538 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp3zsc3sxl/inter.hic" "/tmp/tmp3zsc3sxl/vector.txt" 2021-09-23 21:20:12,358 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 21:20:12,358 DEBUG SimpleSubprocess cp "/tmp/tmp3zsc3sxl/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_norm.hic" 2021-09-23 21:20:12,691 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 21:20:12,744 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/merged_nodups.txt" 2021-09-23 21:20:34,176 INFO SimpleSubprocess CopyResult - 0:00:21 2021-09-23 21:20:34,176 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter.pairs.txt" 2021-09-23 21:20:44,657 INFO SimpleSubprocess CopyResult - 0:00:10 2021-09-23 21:20:44,657 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/vector.txt" 2021-09-23 21:20:44,668 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:44,668 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter.hic" 2021-09-23 21:20:47,036 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-23 21:20:47,037 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_statistics.txt" 2021-09-23 21:20:47,045 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,046 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_no_balanced_5kb.cool" 2021-09-23 21:20:47,164 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,164 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_5kb.cool" 2021-09-23 21:20:47,298 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,299 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_no_balanced_10kb.cool" 2021-09-23 21:20:47,402 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,403 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_10kb.cool" 2021-09-23 21:20:47,534 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,535 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_no_balanced_20kb.cool" 2021-09-23 21:20:47,615 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,615 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_20kb.cool" 2021-09-23 21:20:47,732 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,732 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_no_balanced_25kb.cool" 2021-09-23 21:20:47,815 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,815 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_25kb.cool" 2021-09-23 21:20:47,947 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:47,947 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_no_balanced_50kb.cool" 2021-09-23 21:20:48,048 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:48,048 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/inter_50kb.cool" 2021-09-23 21:20:48,148 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 21:20:48,240 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500320/__temp__" 2021-09-23 21:20:58,430 INFO SimpleSubprocess RemoveTemp - 0:00:10 2021-09-23 21:20:58,430 INFO BenchmarkPipeline 'SRR7500320' FINISHED, SUMMARY TIME - 8:02:32