2021-08-30 08:36:13,361 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099909' --- 2021-08-30 08:36:13,361 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099909.sra 2021-08-30 08:36:13,361 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__ 2021-08-30 08:36:13,361 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpwr30lbab "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099909.sra" 2021-08-30 09:18:55,464 INFO SimpleSubprocess Sra2FastQ - 0:42:42 2021-08-30 09:18:55,479 DEBUG SimpleSubprocess gzip /tmp/tmpwr30lbab/* 2021-08-30 12:35:53,158 INFO SimpleSubprocess GZipFastQ - 3:16:57 2021-08-30 12:35:53,168 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/fastq"; mv /tmp/tmpwr30lbab/SRR5099909_1.fastq.gz /tmp/tmpwr30lbab/SRR5099909_R1.fastq.gz; mv /tmp/tmpwr30lbab/SRR5099909_2.fastq.gz /tmp/tmpwr30lbab/SRR5099909_R2.fastq.gz; cp /tmp/tmpwr30lbab/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/fastq" 2021-08-30 12:41:35,596 INFO SimpleSubprocess CopyFiles - 0:05:42 2021-08-30 12:41:37,698 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__ 2021-08-30 12:41:37,698 INFO Juicer Genome assembly: mm10 2021-08-30 12:41:37,699 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-30 12:41:37,699 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-30 12:41:37,699 INFO Juicer Enzyme: DpnII 2021-08-30 12:41:37,699 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-30 12:41:37,699 INFO Juicer Threads: 10 2021-08-30 12:41:37,699 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/SRR5099909/__temp__" 2021-08-31 03:14:34,324 INFO SimpleSubprocess Juicer - 14:32:56 2021-08-31 03:14:34,544 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/SRR5099909/__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/SRR5099909/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/splits/SRR5099909_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/splits/SRR5099909_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/splits/SRR5099909.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/splits/SRR5099909.fastq.gz.sam done successfully (-: Finished sorting all sorted files into a single merge. WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-30T23:10:14,499] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body ........................................................................................................................................................................................................................................ Writing footer Finished preprocess Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Finished writing norms WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-31T00:33:48,412] [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/SRR5099909/__temp__/aligned/inter_30.hic. Motifs read from /Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/references/motif ARROWHEAD: WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-31T03:14:31,668] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__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/SRR5099909/__temp__/aligned for results 2021-08-31 03:14:34,819 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/merged_nodups.txt 2021-08-31 03:14:34,819 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt 2021-08-31 03:14:35,008 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp34uwpon2/inter.pairs.txt" 2021-08-31 03:17:01,582 INFO SimpleSubprocess MakeInterPairs - 0:02:26 2021-08-31 03:17:01,582 DEBUG SimpleSubprocess cp "/tmp/tmp34uwpon2/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt" 2021-08-31 03:17:03,523 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-31 03:17:04,231 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt 2021-08-31 03:17:04,232 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-31 03:17:04,232 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 03:17:04,232 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 03:17:04,232 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-31 03:17:04,265 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/SRR5099909/__temp__/aligned/inter.pairs.txt" "/tmp/tmpspguiwnb/inter_no_balanced.cool" 2021-08-31 03:18:45,911 INFO SimpleSubprocess MakeCool - 0:01:41 2021-08-31 03:18:45,911 DEBUG SimpleSubprocess cp "/tmp/tmpspguiwnb/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-31 03:18:45,965 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:18:45,978 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt 2021-08-31 03:18:45,987 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-31 03:18:45,987 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 03:18:45,987 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 03:18:45,988 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-31 03:18:46,004 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/SRR5099909/__temp__/aligned/inter.pairs.txt" "/tmp/tmpa8kdeu6k/inter_no_balanced.cool" 2021-08-31 03:20:17,523 INFO SimpleSubprocess MakeCool - 0:01:31 2021-08-31 03:20:17,524 DEBUG SimpleSubprocess cp "/tmp/tmpa8kdeu6k/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-31 03:20:17,552 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:20:17,574 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt 2021-08-31 03:20:17,574 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-31 03:20:17,574 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 03:20:17,574 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 03:20:17,574 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-31 03:20:17,593 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/SRR5099909/__temp__/aligned/inter.pairs.txt" "/tmp/tmpdvlboeub/inter_no_balanced.cool" 2021-08-31 03:21:43,503 INFO SimpleSubprocess MakeCool - 0:01:25 2021-08-31 03:21:43,503 DEBUG SimpleSubprocess cp "/tmp/tmpdvlboeub/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-31 03:21:43,526 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:21:43,529 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt 2021-08-31 03:21:43,529 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-31 03:21:43,529 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 03:21:43,530 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 03:21:43,530 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-31 03:21:43,547 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/SRR5099909/__temp__/aligned/inter.pairs.txt" "/tmp/tmp7b80sqko/inter_no_balanced.cool" 2021-08-31 03:23:09,091 INFO SimpleSubprocess MakeCool - 0:01:25 2021-08-31 03:23:09,092 DEBUG SimpleSubprocess cp "/tmp/tmp7b80sqko/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-31 03:23:09,141 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:23:09,182 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt 2021-08-31 03:23:09,182 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-31 03:23:09,182 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 03:23:09,182 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 03:23:09,182 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-31 03:23:09,188 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/SRR5099909/__temp__/aligned/inter.pairs.txt" "/tmp/tmp0bfv2f7o/inter_no_balanced.cool" 2021-08-31 03:24:29,164 INFO SimpleSubprocess MakeCool - 0:01:19 2021-08-31 03:24:29,165 DEBUG SimpleSubprocess cp "/tmp/tmp0bfv2f7o/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-31 03:24:29,185 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:24:29,243 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-31 03:24:29,243 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_5kb.cool 2021-08-31 03:24:29,243 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 03:24:29,263 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp9mf5yo88/inter.cool" 2021-08-31 03:24:29,297 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 03:24:29,298 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp9mf5yo88/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 03:25:04,281 INFO SimpleSubprocess NormalizeCool - 0:00:34 2021-08-31 03:25:04,293 DEBUG SimpleSubprocess cp "/tmp/tmp9mf5yo88/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_5kb.cool" 2021-08-31 03:25:04,326 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:25:04,343 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-31 03:25:04,343 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_10kb.cool 2021-08-31 03:25:04,343 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 03:25:04,366 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpjpf9vahf/inter.cool" 2021-08-31 03:25:04,397 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 03:25:04,397 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpjpf9vahf/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 03:25:20,119 INFO SimpleSubprocess NormalizeCool - 0:00:15 2021-08-31 03:25:20,120 DEBUG SimpleSubprocess cp "/tmp/tmpjpf9vahf/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_10kb.cool" 2021-08-31 03:25:20,147 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:25:20,175 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-31 03:25:20,175 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_20kb.cool 2021-08-31 03:25:20,175 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 03:25:20,233 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp_bb814y1/inter.cool" 2021-08-31 03:25:20,255 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 03:25:20,256 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp_bb814y1/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 03:25:30,674 INFO SimpleSubprocess NormalizeCool - 0:00:10 2021-08-31 03:25:30,701 DEBUG SimpleSubprocess cp "/tmp/tmp_bb814y1/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_20kb.cool" 2021-08-31 03:25:30,723 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:25:30,755 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-31 03:25:30,756 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_25kb.cool 2021-08-31 03:25:30,756 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 03:25:30,781 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpyld8toqw/inter.cool" 2021-08-31 03:25:30,802 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 03:25:30,802 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpyld8toqw/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 03:25:39,646 INFO SimpleSubprocess NormalizeCool - 0:00:08 2021-08-31 03:25:39,646 DEBUG SimpleSubprocess cp "/tmp/tmpyld8toqw/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_25kb.cool" 2021-08-31 03:25:39,667 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:25:39,693 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-31 03:25:39,693 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_50kb.cool 2021-08-31 03:25:39,693 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 03:25:39,693 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmprmhtpjrh/inter.cool" 2021-08-31 03:25:39,711 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 03:25:39,711 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmprmhtpjrh/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 03:25:44,185 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-08-31 03:25:44,185 DEBUG SimpleSubprocess cp "/tmp/tmprmhtpjrh/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_50kb.cool" 2021-08-31 03:25:44,203 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:25:44,270 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt 2021-08-31 03:25:44,316 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-31 03:25:44,383 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_5kb.cool 2021-08-31 03:25:44,383 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt 2021-08-31 03:25:44,383 INFO AddWeight Chromosome: chr1 2021-08-31 03:25:44,383 INFO AddWeight Resolution [bp]: 5000 2021-08-31 03:25:52,651 INFO AddWeight AddWeight successfully finished 2021-08-31 03:25:52,651 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_10kb.cool 2021-08-31 03:25:52,651 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt 2021-08-31 03:25:52,652 INFO AddWeight Chromosome: chr1 2021-08-31 03:25:52,652 INFO AddWeight Resolution [bp]: 10000 2021-08-31 03:25:52,838 INFO AddWeight AddWeight successfully finished 2021-08-31 03:25:52,838 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_20kb.cool 2021-08-31 03:25:52,838 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt 2021-08-31 03:25:52,839 INFO AddWeight Chromosome: chr1 2021-08-31 03:25:52,839 INFO AddWeight Resolution [bp]: 20000 2021-08-31 03:25:52,960 INFO AddWeight AddWeight successfully finished 2021-08-31 03:25:52,960 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_25kb.cool 2021-08-31 03:25:52,960 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt 2021-08-31 03:25:52,960 INFO AddWeight Chromosome: chr1 2021-08-31 03:25:52,960 INFO AddWeight Resolution [bp]: 25000 2021-08-31 03:25:52,999 INFO AddWeight AddWeight successfully finished 2021-08-31 03:25:53,000 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_50kb.cool 2021-08-31 03:25:53,000 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt 2021-08-31 03:25:53,000 INFO AddWeight Chromosome: chr1 2021-08-31 03:25:53,000 INFO AddWeight Resolution [bp]: 50000 2021-08-31 03:25:53,027 INFO AddWeight AddWeight successfully finished 2021-08-31 03:25:53,152 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.hic 2021-08-31 03:25:53,152 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_norm.hic 2021-08-31 03:25:53,152 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt 2021-08-31 03:25:53,152 INFO Vector2HiC Threads: 10 2021-08-31 03:25:53,384 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.hic" "/tmp/tmpg_3d7mtl/inter.hic" 2021-08-31 03:25:54,861 INFO SimpleSubprocess TempFiles - 0:00:01 2021-08-31 03:25:54,861 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-08-31 03:25:54,863 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpg_3d7mtl/inter.hic" "/tmp/tmpg_3d7mtl/vector.txt" 2021-08-31 03:26:01,545 INFO SimpleSubprocess NormalizeHiC - 0:00:06 2021-08-31 03:26:01,546 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-08-31 03:26:01,547 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpg_3d7mtl/inter.hic" "/tmp/tmpg_3d7mtl/vector.txt" 2021-08-31 03:26:06,004 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-31 03:26:06,005 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-08-31 03:26:06,005 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpg_3d7mtl/inter.hic" "/tmp/tmpg_3d7mtl/vector.txt" 2021-08-31 03:26:09,696 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-31 03:26:09,696 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-08-31 03:26:09,697 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpg_3d7mtl/inter.hic" "/tmp/tmpg_3d7mtl/vector.txt" 2021-08-31 03:26:13,743 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-31 03:26:13,743 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-08-31 03:26:13,743 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpg_3d7mtl/inter.hic" "/tmp/tmpg_3d7mtl/vector.txt" 2021-08-31 03:26:17,648 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-31 03:26:17,648 DEBUG SimpleSubprocess cp "/tmp/tmpg_3d7mtl/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_norm.hic" 2021-08-31 03:26:18,039 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 03:26:18,203 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/merged_nodups.txt" 2021-08-31 03:29:56,510 INFO SimpleSubprocess CopyResult - 0:03:38 2021-08-31 03:29:56,546 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter.pairs.txt" 2021-08-31 03:30:08,764 INFO SimpleSubprocess CopyResult - 0:00:12 2021-08-31 03:30:08,764 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/vector.txt" 2021-08-31 03:30:08,833 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:08,834 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter.hic" 2021-08-31 03:30:12,421 INFO SimpleSubprocess CopyResult - 0:00:03 2021-08-31 03:30:12,422 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_statistics.txt" 2021-08-31 03:30:12,506 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:12,506 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_no_balanced_5kb.cool" 2021-08-31 03:30:12,727 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:12,728 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_5kb.cool" 2021-08-31 03:30:13,037 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:13,038 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_no_balanced_10kb.cool" 2021-08-31 03:30:13,322 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:13,322 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_10kb.cool" 2021-08-31 03:30:13,556 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:13,556 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_no_balanced_20kb.cool" 2021-08-31 03:30:13,792 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:13,792 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_20kb.cool" 2021-08-31 03:30:13,991 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:13,991 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_no_balanced_25kb.cool" 2021-08-31 03:30:14,135 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:14,135 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_25kb.cool" 2021-08-31 03:30:14,281 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:14,282 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_no_balanced_50kb.cool" 2021-08-31 03:30:14,442 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:14,442 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/inter_50kb.cool" 2021-08-31 03:30:14,790 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 03:30:15,003 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__" 2021-08-31 03:30:42,700 INFO SimpleSubprocess RemoveTemp - 0:00:27 2021-08-31 03:30:42,700 INFO BenchmarkPipeline 'SRR5099909' FINISHED, SUMMARY TIME - 18:54:29 2021-09-01 12:23:13,426 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099909' --- 2021-09-01 12:23:13,440 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__" 2021-09-01 12:23:13,448 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,448 INFO BenchmarkPipeline 'SRR5099909' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,845 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099909' --- 2021-09-02 13:38:17,845 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099909/__temp__" 2021-09-02 13:38:17,853 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,854 INFO BenchmarkPipeline 'SRR5099909' FINISHED, SUMMARY TIME - 0:00:00