2021-08-31 19:21:01,100 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099911' --- 2021-08-31 19:21:01,106 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099911.sra 2021-08-31 19:21:01,106 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__ 2021-08-31 19:21:01,197 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpzlg78n7f "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099911.sra" 2021-08-31 19:58:02,842 INFO SimpleSubprocess Sra2FastQ - 0:37:01 2021-08-31 19:58:02,852 DEBUG SimpleSubprocess gzip /tmp/tmpzlg78n7f/* 2021-08-31 22:30:33,216 INFO SimpleSubprocess GZipFastQ - 2:32:30 2021-08-31 22:30:33,500 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/fastq"; mv /tmp/tmpzlg78n7f/SRR5099911_1.fastq.gz /tmp/tmpzlg78n7f/SRR5099911_R1.fastq.gz; mv /tmp/tmpzlg78n7f/SRR5099911_2.fastq.gz /tmp/tmpzlg78n7f/SRR5099911_R2.fastq.gz; cp /tmp/tmpzlg78n7f/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/fastq" 2021-08-31 22:34:21,720 INFO SimpleSubprocess CopyFiles - 0:03:48 2021-08-31 22:34:23,861 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__ 2021-08-31 22:34:23,862 INFO Juicer Genome assembly: mm10 2021-08-31 22:34:23,862 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-31 22:34:23,862 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 22:34:23,862 INFO Juicer Enzyme: DpnII 2021-08-31 22:34:23,862 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-31 22:34:23,862 INFO Juicer Threads: 10 2021-08-31 22:34:23,862 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/SRR5099911/__temp__" 2021-09-01 07:40:45,053 INFO SimpleSubprocess Juicer - 9:06:21 2021-09-01 07:40:45,067 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/SRR5099911/__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/SRR5099911/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/splits/SRR5099911_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/splits/SRR5099911_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/splits/SRR5099911.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/splits/SRR5099911.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 [2021-09-01T06:10:51,894] [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 [2021-09-01T07:02:01,399] [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/SRR5099911/__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 [2021-09-01T07:40:44,753] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__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/SRR5099911/__temp__/aligned for results 2021-09-01 07:40:45,157 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/merged_nodups.txt 2021-09-01 07:40:45,158 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt 2021-09-01 07:40:45,158 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp2f_4aud4/inter.pairs.txt" 2021-09-01 07:41:56,409 INFO SimpleSubprocess MakeInterPairs - 0:01:11 2021-09-01 07:41:56,409 DEBUG SimpleSubprocess cp "/tmp/tmp2f_4aud4/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt" 2021-09-01 07:41:58,023 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-01 07:41:58,252 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt 2021-09-01 07:41:58,252 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-01 07:41:58,252 INFO Pairs2Cool Genome assembly: mm10 2021-09-01 07:41:58,252 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-01 07:41:58,252 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-01 07:41:58,253 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/SRR5099911/__temp__/aligned/inter.pairs.txt" "/tmp/tmp6yxtdwec/inter_no_balanced.cool" 2021-09-01 07:43:33,484 INFO SimpleSubprocess MakeCool - 0:01:35 2021-09-01 07:43:33,484 DEBUG SimpleSubprocess cp "/tmp/tmp6yxtdwec/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-01 07:43:33,519 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:43:33,523 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt 2021-09-01 07:43:33,523 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-01 07:43:33,523 INFO Pairs2Cool Genome assembly: mm10 2021-09-01 07:43:33,523 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-01 07:43:33,523 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-01 07:43:33,523 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/SRR5099911/__temp__/aligned/inter.pairs.txt" "/tmp/tmpc5948xp5/inter_no_balanced.cool" 2021-09-01 07:44:59,772 INFO SimpleSubprocess MakeCool - 0:01:26 2021-09-01 07:44:59,772 DEBUG SimpleSubprocess cp "/tmp/tmpc5948xp5/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-01 07:44:59,799 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:44:59,826 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt 2021-09-01 07:44:59,826 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-01 07:44:59,826 INFO Pairs2Cool Genome assembly: mm10 2021-09-01 07:44:59,826 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-01 07:44:59,826 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-01 07:44:59,853 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/SRR5099911/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2lfvqt85/inter_no_balanced.cool" 2021-09-01 07:46:22,401 INFO SimpleSubprocess MakeCool - 0:01:22 2021-09-01 07:46:22,401 DEBUG SimpleSubprocess cp "/tmp/tmp2lfvqt85/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-01 07:46:22,424 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:46:22,448 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt 2021-09-01 07:46:22,449 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-01 07:46:22,449 INFO Pairs2Cool Genome assembly: mm10 2021-09-01 07:46:22,449 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-01 07:46:22,449 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-01 07:46:22,473 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/SRR5099911/__temp__/aligned/inter.pairs.txt" "/tmp/tmpuavcntqr/inter_no_balanced.cool" 2021-09-01 07:47:43,213 INFO SimpleSubprocess MakeCool - 0:01:20 2021-09-01 07:47:43,214 DEBUG SimpleSubprocess cp "/tmp/tmpuavcntqr/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-01 07:47:43,235 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:47:43,264 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt 2021-09-01 07:47:43,264 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-01 07:47:43,264 INFO Pairs2Cool Genome assembly: mm10 2021-09-01 07:47:43,264 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-01 07:47:43,264 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-01 07:47:43,294 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/SRR5099911/__temp__/aligned/inter.pairs.txt" "/tmp/tmppem7zpl5/inter_no_balanced.cool" 2021-09-01 07:49:00,858 INFO SimpleSubprocess MakeCool - 0:01:17 2021-09-01 07:49:00,858 DEBUG SimpleSubprocess cp "/tmp/tmppem7zpl5/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-01 07:49:00,878 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:49:00,883 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-01 07:49:00,883 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_5kb.cool 2021-09-01 07:49:00,883 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-09-01 07:49:00,883 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpfqvq52ay/inter.cool" 2021-09-01 07:49:00,918 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-01 07:49:00,918 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpfqvq52ay/inter.cool" "chr1:70,945,000-81,010,000" 2021-09-01 07:49:08,718 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-01 07:49:08,718 DEBUG SimpleSubprocess cp "/tmp/tmpfqvq52ay/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_5kb.cool" 2021-09-01 07:49:08,753 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:49:08,790 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-01 07:49:08,790 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_10kb.cool 2021-09-01 07:49:08,790 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-09-01 07:49:08,814 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpm3d6709q/inter.cool" 2021-09-01 07:49:08,843 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-01 07:49:08,843 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpm3d6709q/inter.cool" "chr1:70,945,000-81,010,000" 2021-09-01 07:49:13,539 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-01 07:49:13,539 DEBUG SimpleSubprocess cp "/tmp/tmpm3d6709q/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_10kb.cool" 2021-09-01 07:49:13,566 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:49:13,600 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-01 07:49:13,600 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_20kb.cool 2021-09-01 07:49:13,600 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-09-01 07:49:13,628 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpyrbwtlnx/inter.cool" 2021-09-01 07:49:13,651 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-01 07:49:13,651 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpyrbwtlnx/inter.cool" "chr1:70,945,000-81,010,000" 2021-09-01 07:49:17,171 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-01 07:49:17,172 DEBUG SimpleSubprocess cp "/tmp/tmpyrbwtlnx/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_20kb.cool" 2021-09-01 07:49:17,197 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:49:17,199 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-01 07:49:17,200 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_25kb.cool 2021-09-01 07:49:17,200 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-09-01 07:49:17,222 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp954x7z0b/inter.cool" 2021-09-01 07:49:17,245 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-01 07:49:17,246 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp954x7z0b/inter.cool" "chr1:70,945,000-81,010,000" 2021-09-01 07:49:20,617 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-01 07:49:20,617 DEBUG SimpleSubprocess cp "/tmp/tmp954x7z0b/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_25kb.cool" 2021-09-01 07:49:20,639 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:49:20,642 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-01 07:49:20,642 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_50kb.cool 2021-09-01 07:49:20,642 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-09-01 07:49:20,642 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp2vtilaid/inter.cool" 2021-09-01 07:49:20,661 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-01 07:49:20,661 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp2vtilaid/inter.cool" "chr1:70,945,000-81,010,000" 2021-09-01 07:49:22,608 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-01 07:49:22,608 DEBUG SimpleSubprocess cp "/tmp/tmp2vtilaid/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_50kb.cool" 2021-09-01 07:49:22,648 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:49:22,680 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt 2021-09-01 07:49:22,686 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-01 07:49:22,687 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_5kb.cool 2021-09-01 07:49:22,687 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt 2021-09-01 07:49:22,687 INFO AddWeight Chromosome: chr1 2021-09-01 07:49:22,687 INFO AddWeight Resolution [bp]: 5000 2021-09-01 07:49:22,956 INFO AddWeight AddWeight successfully finished 2021-09-01 07:49:22,956 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_10kb.cool 2021-09-01 07:49:22,956 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt 2021-09-01 07:49:22,956 INFO AddWeight Chromosome: chr1 2021-09-01 07:49:22,956 INFO AddWeight Resolution [bp]: 10000 2021-09-01 07:49:23,024 INFO AddWeight AddWeight successfully finished 2021-09-01 07:49:23,024 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_20kb.cool 2021-09-01 07:49:23,024 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt 2021-09-01 07:49:23,024 INFO AddWeight Chromosome: chr1 2021-09-01 07:49:23,024 INFO AddWeight Resolution [bp]: 20000 2021-09-01 07:49:23,065 INFO AddWeight AddWeight successfully finished 2021-09-01 07:49:23,065 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_25kb.cool 2021-09-01 07:49:23,065 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt 2021-09-01 07:49:23,065 INFO AddWeight Chromosome: chr1 2021-09-01 07:49:23,065 INFO AddWeight Resolution [bp]: 25000 2021-09-01 07:49:23,100 INFO AddWeight AddWeight successfully finished 2021-09-01 07:49:23,100 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_50kb.cool 2021-09-01 07:49:23,100 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt 2021-09-01 07:49:23,100 INFO AddWeight Chromosome: chr1 2021-09-01 07:49:23,100 INFO AddWeight Resolution [bp]: 50000 2021-09-01 07:49:23,125 INFO AddWeight AddWeight successfully finished 2021-09-01 07:49:23,126 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.hic 2021-09-01 07:49:23,127 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_norm.hic 2021-09-01 07:49:23,127 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt 2021-09-01 07:49:23,127 INFO Vector2HiC Threads: 10 2021-09-01 07:49:23,157 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.hic" "/tmp/tmpt0cunkje/inter.hic" 2021-09-01 07:49:23,448 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-01 07:49:23,449 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-09-01 07:49:23,451 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0cunkje/inter.hic" "/tmp/tmpt0cunkje/vector.txt" 2021-09-01 07:49:28,359 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-01 07:49:28,359 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-09-01 07:49:28,361 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0cunkje/inter.hic" "/tmp/tmpt0cunkje/vector.txt" 2021-09-01 07:49:32,727 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-01 07:49:32,727 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-09-01 07:49:32,728 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0cunkje/inter.hic" "/tmp/tmpt0cunkje/vector.txt" 2021-09-01 07:49:36,503 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-01 07:49:36,503 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-09-01 07:49:36,504 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0cunkje/inter.hic" "/tmp/tmpt0cunkje/vector.txt" 2021-09-01 07:49:40,615 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-01 07:49:40,615 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-09-01 07:49:40,616 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0cunkje/inter.hic" "/tmp/tmpt0cunkje/vector.txt" 2021-09-01 07:49:44,747 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-01 07:49:44,747 DEBUG SimpleSubprocess cp "/tmp/tmpt0cunkje/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_norm.hic" 2021-09-01 07:49:45,141 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-01 07:49:45,281 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/merged_nodups.txt" 2021-09-01 07:51:40,421 INFO SimpleSubprocess CopyResult - 0:01:55 2021-09-01 07:51:40,442 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter.pairs.txt" 2021-09-01 07:51:53,043 INFO SimpleSubprocess CopyResult - 0:00:12 2021-09-01 07:51:53,043 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/vector.txt" 2021-09-01 07:51:53,183 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:53,183 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter.hic" 2021-09-01 07:51:56,803 INFO SimpleSubprocess CopyResult - 0:00:03 2021-09-01 07:51:56,804 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_statistics.txt" 2021-09-01 07:51:56,812 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:56,812 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_no_balanced_5kb.cool" 2021-09-01 07:51:57,610 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:57,610 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_5kb.cool" 2021-09-01 07:51:57,834 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:57,834 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_no_balanced_10kb.cool" 2021-09-01 07:51:58,121 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:58,121 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_10kb.cool" 2021-09-01 07:51:58,384 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:58,384 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_no_balanced_20kb.cool" 2021-09-01 07:51:58,527 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:58,527 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_20kb.cool" 2021-09-01 07:51:58,719 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:58,720 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_no_balanced_25kb.cool" 2021-09-01 07:51:58,903 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:58,904 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_25kb.cool" 2021-09-01 07:51:59,235 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:59,235 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_no_balanced_50kb.cool" 2021-09-01 07:51:59,587 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:51:59,587 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/inter_50kb.cool" 2021-09-01 07:51:59,852 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-01 07:52:00,099 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__" 2021-09-01 07:52:19,831 INFO SimpleSubprocess RemoveTemp - 0:00:19 2021-09-01 07:52:19,831 INFO BenchmarkPipeline 'SRR5099911' FINISHED, SUMMARY TIME - 12:31:18 2021-09-01 12:23:13,478 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099911' --- 2021-09-01 12:23:13,479 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__" 2021-09-01 12:23:13,488 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,488 INFO BenchmarkPipeline 'SRR5099911' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,862 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099911' --- 2021-09-02 13:38:17,862 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099911/__temp__" 2021-09-02 13:38:17,869 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,869 INFO BenchmarkPipeline 'SRR5099911' FINISHED, SUMMARY TIME - 0:00:00