2021-08-29 10:05:12,063 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099904' --- 2021-08-29 10:05:12,063 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099904.sra 2021-08-29 10:05:12,063 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__ 2021-08-29 10:05:12,063 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmppcwrn4dz "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099904.sra" 2021-08-29 10:21:48,365 INFO SimpleSubprocess Sra2FastQ - 0:16:36 2021-08-29 10:21:48,365 DEBUG SimpleSubprocess gzip /tmp/tmppcwrn4dz/* 2021-08-29 10:59:25,273 INFO SimpleSubprocess GZipFastQ - 0:37:36 2021-08-29 10:59:25,302 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/fastq"; mv /tmp/tmppcwrn4dz/SRR5099904_2.fastq.gz /tmp/tmppcwrn4dz/SRR5099904_R2.fastq.gz; mv /tmp/tmppcwrn4dz/SRR5099904_1.fastq.gz /tmp/tmppcwrn4dz/SRR5099904_R1.fastq.gz; cp /tmp/tmppcwrn4dz/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/fastq" 2021-08-29 10:59:32,237 INFO SimpleSubprocess CopyFiles - 0:00:06 2021-08-29 10:59:33,279 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__ 2021-08-29 10:59:33,279 INFO Juicer Genome assembly: hg38 2021-08-29 10:59:33,279 INFO Juicer Genome FASTA path: /Data/DataBases/hg38/hg38_canonic.fa 2021-08-29 10:59:33,279 INFO Juicer Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 10:59:33,279 INFO Juicer Enzyme: DpnII 2021-08-29 10:59:33,279 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt 2021-08-29 10:59:33,279 INFO Juicer Threads: 10 2021-08-29 10:59:33,279 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 hg38 -z "/Data/DataBases/hg38/hg38_canonic.fa" -p "/Data/DataBases/hg38/hg38_canonic.chrom.sizes" -s DpnII -y "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt" -d "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__" 2021-08-29 15:08:15,697 INFO SimpleSubprocess Juicer - 4:08:42 2021-08-29 15:08:15,717 INFO Juicer Using /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt as site file (-: Looking for fastq files...fastq files exist (-: Aligning files matching /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/fastq/*_R*.fastq* to genome hg38 with site file /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt (-: Created /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/hg38/hg38_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/splits/SRR5099904_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/splits/SRR5099904_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/splits/SRR5099904.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/splits/SRR5099904.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 [2021-08-29T14:27:01,347] [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 [2021-08-29T14:49:48,330] [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 hg38 Data read from /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__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 [2021-08-29T15:08:15,209] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__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/SRR5099904/__temp__/aligned for results 2021-08-29 15:08:15,771 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/merged_nodups.txt 2021-08-29 15:08:15,771 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt 2021-08-29 15:08:15,797 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/merged_nodups.txt" > "/tmp/tmph1okk9c4/inter.pairs.txt" 2021-08-29 15:08:51,020 INFO SimpleSubprocess MakeInterPairs - 0:00:35 2021-08-29 15:08:51,020 DEBUG SimpleSubprocess cp "/tmp/tmph1okk9c4/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt" 2021-08-29 15:08:51,953 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:08:52,805 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt 2021-08-29 15:08:52,805 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 15:08:52,805 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 15:08:52,805 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 15:08:52,805 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-29 15:08:52,806 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":5000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt" "/tmp/tmpjnsobvlz/inter_no_balanced.cool" 2021-08-29 15:09:54,488 INFO SimpleSubprocess MakeCool - 0:01:01 2021-08-29 15:09:54,488 DEBUG SimpleSubprocess cp "/tmp/tmpjnsobvlz/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-29 15:09:54,514 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:09:54,517 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt 2021-08-29 15:09:54,517 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 15:09:54,518 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 15:09:54,518 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 15:09:54,518 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-29 15:09:54,549 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":10000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt" "/tmp/tmp80xps5i5/inter_no_balanced.cool" 2021-08-29 15:10:46,812 INFO SimpleSubprocess MakeCool - 0:00:52 2021-08-29 15:10:46,812 DEBUG SimpleSubprocess cp "/tmp/tmp80xps5i5/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-29 15:10:46,832 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:10:46,834 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt 2021-08-29 15:10:46,835 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 15:10:46,835 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 15:10:46,835 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 15:10:46,835 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-29 15:10:46,846 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":20000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt" "/tmp/tmp50ghi1a_/inter_no_balanced.cool" 2021-08-29 15:11:35,741 INFO SimpleSubprocess MakeCool - 0:00:48 2021-08-29 15:11:35,741 DEBUG SimpleSubprocess cp "/tmp/tmp50ghi1a_/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-29 15:11:35,759 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:11:35,761 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt 2021-08-29 15:11:35,761 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 15:11:35,761 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 15:11:35,761 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 15:11:35,761 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-29 15:11:35,762 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":25000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt" "/tmp/tmpv60e5xec/inter_no_balanced.cool" 2021-08-29 15:12:25,979 INFO SimpleSubprocess MakeCool - 0:00:50 2021-08-29 15:12:25,979 DEBUG SimpleSubprocess cp "/tmp/tmpv60e5xec/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-29 15:12:25,996 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:12:25,998 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt 2021-08-29 15:12:25,998 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 15:12:25,998 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 15:12:25,998 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 15:12:25,998 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-29 15:12:25,998 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":50000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt" "/tmp/tmp_tblzazc/inter_no_balanced.cool" 2021-08-29 15:13:12,248 INFO SimpleSubprocess MakeCool - 0:00:46 2021-08-29 15:13:12,248 DEBUG SimpleSubprocess cp "/tmp/tmp_tblzazc/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-29 15:13:12,264 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:13:12,268 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 15:13:12,268 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_5kb.cool 2021-08-29 15:13:12,268 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 15:13:12,284 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpvx6uzu5f/inter.cool" 2021-08-29 15:13:12,310 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 15:13:12,310 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpvx6uzu5f/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 15:13:25,565 INFO SimpleSubprocess NormalizeCool - 0:00:13 2021-08-29 15:13:25,565 DEBUG SimpleSubprocess cp "/tmp/tmpvx6uzu5f/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_5kb.cool" 2021-08-29 15:13:25,589 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:13:25,592 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 15:13:25,592 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_10kb.cool 2021-08-29 15:13:25,592 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 15:13:25,592 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp08_j326n/inter.cool" 2021-08-29 15:13:25,612 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 15:13:25,613 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp08_j326n/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 15:13:28,928 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-29 15:13:28,928 DEBUG SimpleSubprocess cp "/tmp/tmp08_j326n/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_10kb.cool" 2021-08-29 15:13:28,948 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:13:28,951 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 15:13:28,951 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_20kb.cool 2021-08-29 15:13:28,951 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 15:13:28,951 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpifnsvaaj/inter.cool" 2021-08-29 15:13:28,969 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 15:13:28,969 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpifnsvaaj/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 15:13:31,287 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-29 15:13:31,287 DEBUG SimpleSubprocess cp "/tmp/tmpifnsvaaj/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_20kb.cool" 2021-08-29 15:13:31,306 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:13:31,309 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 15:13:31,309 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_25kb.cool 2021-08-29 15:13:31,309 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 15:13:31,309 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpsynvco6a/inter.cool" 2021-08-29 15:13:31,326 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 15:13:31,326 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpsynvco6a/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 15:13:33,540 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-29 15:13:33,540 DEBUG SimpleSubprocess cp "/tmp/tmpsynvco6a/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_25kb.cool" 2021-08-29 15:13:33,558 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:13:33,560 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 15:13:33,560 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_50kb.cool 2021-08-29 15:13:33,560 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 15:13:33,560 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpzz4ye485/inter.cool" 2021-08-29 15:13:33,576 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 15:13:33,576 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpzz4ye485/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 15:13:35,112 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 15:13:35,112 DEBUG SimpleSubprocess cp "/tmp/tmpzz4ye485/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_50kb.cool" 2021-08-29 15:13:35,127 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:13:35,130 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt 2021-08-29 15:13:35,136 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-29 15:13:35,137 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_5kb.cool 2021-08-29 15:13:35,137 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt 2021-08-29 15:13:35,137 INFO AddWeight Chromosome: chr2 2021-08-29 15:13:35,137 INFO AddWeight Resolution [bp]: 5000 2021-08-29 15:13:36,199 INFO AddWeight AddWeight successfully finished 2021-08-29 15:13:36,199 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_10kb.cool 2021-08-29 15:13:36,199 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt 2021-08-29 15:13:36,199 INFO AddWeight Chromosome: chr2 2021-08-29 15:13:36,199 INFO AddWeight Resolution [bp]: 10000 2021-08-29 15:13:36,312 INFO AddWeight AddWeight successfully finished 2021-08-29 15:13:36,312 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_20kb.cool 2021-08-29 15:13:36,312 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt 2021-08-29 15:13:36,312 INFO AddWeight Chromosome: chr2 2021-08-29 15:13:36,313 INFO AddWeight Resolution [bp]: 20000 2021-08-29 15:13:36,360 INFO AddWeight AddWeight successfully finished 2021-08-29 15:13:36,361 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_25kb.cool 2021-08-29 15:13:36,361 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt 2021-08-29 15:13:36,361 INFO AddWeight Chromosome: chr2 2021-08-29 15:13:36,361 INFO AddWeight Resolution [bp]: 25000 2021-08-29 15:13:36,402 INFO AddWeight AddWeight successfully finished 2021-08-29 15:13:36,402 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_50kb.cool 2021-08-29 15:13:36,402 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt 2021-08-29 15:13:36,402 INFO AddWeight Chromosome: chr2 2021-08-29 15:13:36,402 INFO AddWeight Resolution [bp]: 50000 2021-08-29 15:13:36,456 INFO AddWeight AddWeight successfully finished 2021-08-29 15:13:36,458 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.hic 2021-08-29 15:13:36,458 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_norm.hic 2021-08-29 15:13:36,458 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt 2021-08-29 15:13:36,458 INFO Vector2HiC Threads: 10 2021-08-29 15:13:36,525 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.hic" "/tmp/tmpn_0e_j62/inter.hic" 2021-08-29 15:13:36,769 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 15:13:36,769 INFO Vector2HiC Vector: vector c-tale_normalization chr2 5000 BP 2021-08-29 15:13:36,770 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpn_0e_j62/inter.hic" "/tmp/tmpn_0e_j62/vector.txt" 2021-08-29 15:13:41,493 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 15:13:41,493 INFO Vector2HiC Vector: vector c-tale_normalization chr2 10000 BP 2021-08-29 15:13:41,512 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpn_0e_j62/inter.hic" "/tmp/tmpn_0e_j62/vector.txt" 2021-08-29 15:13:45,535 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 15:13:45,535 INFO Vector2HiC Vector: vector c-tale_normalization chr2 20000 BP 2021-08-29 15:13:45,536 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpn_0e_j62/inter.hic" "/tmp/tmpn_0e_j62/vector.txt" 2021-08-29 15:13:49,393 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 15:13:49,393 INFO Vector2HiC Vector: vector c-tale_normalization chr2 25000 BP 2021-08-29 15:13:49,394 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpn_0e_j62/inter.hic" "/tmp/tmpn_0e_j62/vector.txt" 2021-08-29 15:13:53,484 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 15:13:53,484 INFO Vector2HiC Vector: vector c-tale_normalization chr2 50000 BP 2021-08-29 15:13:53,485 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpn_0e_j62/inter.hic" "/tmp/tmpn_0e_j62/vector.txt" 2021-08-29 15:13:57,534 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 15:13:57,535 DEBUG SimpleSubprocess cp "/tmp/tmpn_0e_j62/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_norm.hic" 2021-08-29 15:13:57,886 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 15:13:57,938 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/merged_nodups.txt" 2021-08-29 15:14:04,502 INFO SimpleSubprocess CopyResult - 0:00:06 2021-08-29 15:14:04,503 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter.pairs.txt" 2021-08-29 15:14:07,180 INFO SimpleSubprocess CopyResult - 0:00:02 2021-08-29 15:14:07,180 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/vector.txt" 2021-08-29 15:14:07,189 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:07,189 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter.hic" 2021-08-29 15:14:08,797 INFO SimpleSubprocess CopyResult - 0:00:01 2021-08-29 15:14:08,797 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_statistics.txt" 2021-08-29 15:14:08,805 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:08,805 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_no_balanced_5kb.cool" 2021-08-29 15:14:08,887 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:08,887 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_5kb.cool" 2021-08-29 15:14:08,960 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:08,960 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_no_balanced_10kb.cool" 2021-08-29 15:14:09,019 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,019 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_10kb.cool" 2021-08-29 15:14:09,076 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,076 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_no_balanced_20kb.cool" 2021-08-29 15:14:09,123 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,123 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_20kb.cool" 2021-08-29 15:14:09,168 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,169 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_no_balanced_25kb.cool" 2021-08-29 15:14:09,205 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,205 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_25kb.cool" 2021-08-29 15:14:09,251 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,251 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_no_balanced_50kb.cool" 2021-08-29 15:14:09,284 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,284 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/inter_50kb.cool" 2021-08-29 15:14:09,309 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 15:14:09,313 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__" 2021-08-29 15:14:17,146 INFO SimpleSubprocess RemoveTemp - 0:00:07 2021-08-29 15:14:17,146 INFO BenchmarkPipeline 'SRR5099904' FINISHED, SUMMARY TIME - 5:09:05 2021-09-01 12:23:13,367 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099904' --- 2021-09-01 12:23:13,367 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__" 2021-09-01 12:23:13,376 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,376 INFO BenchmarkPipeline 'SRR5099904' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,818 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099904' --- 2021-09-02 13:38:17,818 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099904/__temp__" 2021-09-02 13:38:17,826 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,827 INFO BenchmarkPipeline 'SRR5099904' FINISHED, SUMMARY TIME - 0:00:00