2021-08-26 04:51:18,718 INFO BenchmarkPipeline --- START PROCESSING 'SRR7500316' --- 2021-08-26 04:51:18,718 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500316.sra 2021-08-26 04:51:18,718 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__ 2021-08-26 04:51:18,719 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpjef833vp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500316.sra" 2021-08-26 05:12:48,770 INFO SimpleSubprocess Sra2FastQ - 0:21:30 2021-08-26 05:12:48,782 DEBUG SimpleSubprocess gzip /tmp/tmpjef833vp/* 2021-08-26 06:12:21,096 INFO SimpleSubprocess GZipFastQ - 0:59:32 2021-08-26 06:12:21,107 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/fastq"; mv /tmp/tmpjef833vp/SRR7500316_1.fastq.gz /tmp/tmpjef833vp/SRR7500316_R1.fastq.gz; mv /tmp/tmpjef833vp/SRR7500316_2.fastq.gz /tmp/tmpjef833vp/SRR7500316_R2.fastq.gz; cp /tmp/tmpjef833vp/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/fastq" 2021-08-26 06:13:07,618 INFO SimpleSubprocess CopyFiles - 0:00:46 2021-08-26 06:13:09,167 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__ 2021-08-26 06:13:09,167 INFO Juicer Genome assembly: mm10 2021-08-26 06:13:09,167 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-26 06:13:09,167 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 06:13:09,167 INFO Juicer Enzyme: DpnII 2021-08-26 06:13:09,167 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-26 06:13:09,168 INFO Juicer Threads: 10 2021-08-26 06:13:09,168 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/SRR7500316/__temp__" 2021-08-26 12:10:13,674 INFO SimpleSubprocess Juicer - 5:57:04 2021-08-26 12:10:13,708 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/SRR7500316/__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/SRR7500316/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/splits/SRR7500316_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/splits/SRR7500316_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/splits/SRR7500316.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/splits/SRR7500316.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 [2021-08-26T10:35:22,148] [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 [2021-08-26T11:17:55,831] [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/SRR7500316/__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 [2021-08-26T12:10:13,225] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__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/SRR7500316/__temp__/aligned for results 2021-08-26 12:10:13,783 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/merged_nodups.txt 2021-08-26 12:10:13,783 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt 2021-08-26 12:10:13,784 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpnjhs6fqo/inter.pairs.txt" 2021-08-26 12:10:58,466 INFO SimpleSubprocess MakeInterPairs - 0:00:44 2021-08-26 12:10:58,466 DEBUG SimpleSubprocess cp "/tmp/tmpnjhs6fqo/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt" 2021-08-26 12:10:59,697 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-26 12:10:59,880 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt 2021-08-26 12:10:59,880 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-26 12:10:59,880 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 12:10:59,880 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 12:10:59,880 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-26 12:10:59,880 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/SRR7500316/__temp__/aligned/inter.pairs.txt" "/tmp/tmplh_d5rux/inter_no_balanced.cool" 2021-08-26 12:12:09,353 INFO SimpleSubprocess MakeCool - 0:01:09 2021-08-26 12:12:09,353 DEBUG SimpleSubprocess cp "/tmp/tmplh_d5rux/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-26 12:12:09,401 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:12:09,404 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt 2021-08-26 12:12:09,404 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-26 12:12:09,404 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 12:12:09,404 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 12:12:09,404 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-26 12:12:09,405 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/SRR7500316/__temp__/aligned/inter.pairs.txt" "/tmp/tmpflh3cj5q/inter_no_balanced.cool" 2021-08-26 12:13:11,209 INFO SimpleSubprocess MakeCool - 0:01:01 2021-08-26 12:13:11,209 DEBUG SimpleSubprocess cp "/tmp/tmpflh3cj5q/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-26 12:13:11,239 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:13:11,242 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt 2021-08-26 12:13:11,242 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-26 12:13:11,242 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 12:13:11,242 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 12:13:11,242 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-26 12:13:11,243 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/SRR7500316/__temp__/aligned/inter.pairs.txt" "/tmp/tmpsh0e0u3q/inter_no_balanced.cool" 2021-08-26 12:14:09,413 INFO SimpleSubprocess MakeCool - 0:00:58 2021-08-26 12:14:09,414 DEBUG SimpleSubprocess cp "/tmp/tmpsh0e0u3q/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-26 12:14:09,447 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:14:09,449 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt 2021-08-26 12:14:09,449 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-26 12:14:09,449 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 12:14:09,449 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 12:14:09,449 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-26 12:14:09,450 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/SRR7500316/__temp__/aligned/inter.pairs.txt" "/tmp/tmpq1cj3nbu/inter_no_balanced.cool" 2021-08-26 12:15:06,554 INFO SimpleSubprocess MakeCool - 0:00:57 2021-08-26 12:15:06,554 DEBUG SimpleSubprocess cp "/tmp/tmpq1cj3nbu/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-26 12:15:06,573 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:15:06,575 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt 2021-08-26 12:15:06,575 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-26 12:15:06,575 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 12:15:06,576 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 12:15:06,576 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-26 12:15:06,576 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/SRR7500316/__temp__/aligned/inter.pairs.txt" "/tmp/tmp8ap_98zd/inter_no_balanced.cool" 2021-08-26 12:16:01,495 INFO SimpleSubprocess MakeCool - 0:00:54 2021-08-26 12:16:01,495 DEBUG SimpleSubprocess cp "/tmp/tmp8ap_98zd/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-26 12:16:01,513 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:16:01,517 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-26 12:16:01,517 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_5kb.cool 2021-08-26 12:16:01,517 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 12:16:01,517 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpxzvsf7q_/inter.cool" 2021-08-26 12:16:01,545 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 12:16:01,545 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpxzvsf7q_/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 12:16:22,162 INFO SimpleSubprocess NormalizeCool - 0:00:20 2021-08-26 12:16:22,162 DEBUG SimpleSubprocess cp "/tmp/tmpxzvsf7q_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_5kb.cool" 2021-08-26 12:16:22,188 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:16:22,191 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-26 12:16:22,191 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_10kb.cool 2021-08-26 12:16:22,191 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 12:16:22,192 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp7xh97e7a/inter.cool" 2021-08-26 12:16:22,214 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 12:16:22,214 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp7xh97e7a/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 12:16:25,818 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-26 12:16:25,818 DEBUG SimpleSubprocess cp "/tmp/tmp7xh97e7a/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_10kb.cool" 2021-08-26 12:16:25,841 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:16:25,844 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-26 12:16:25,844 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_20kb.cool 2021-08-26 12:16:25,844 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 12:16:25,844 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpv0ki9ob6/inter.cool" 2021-08-26 12:16:25,865 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 12:16:25,865 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpv0ki9ob6/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 12:16:28,535 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-26 12:16:28,535 DEBUG SimpleSubprocess cp "/tmp/tmpv0ki9ob6/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_20kb.cool" 2021-08-26 12:16:28,555 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:16:28,557 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-26 12:16:28,557 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_25kb.cool 2021-08-26 12:16:28,558 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 12:16:28,558 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpny20484a/inter.cool" 2021-08-26 12:16:28,576 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 12:16:28,576 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpny20484a/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 12:16:31,042 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-26 12:16:31,042 DEBUG SimpleSubprocess cp "/tmp/tmpny20484a/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_25kb.cool" 2021-08-26 12:16:31,061 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:16:31,063 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-26 12:16:31,063 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_50kb.cool 2021-08-26 12:16:31,064 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 12:16:31,064 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpljvcm9qj/inter.cool" 2021-08-26 12:16:31,080 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 12:16:31,081 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpljvcm9qj/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 12:16:32,742 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-26 12:16:32,742 DEBUG SimpleSubprocess cp "/tmp/tmpljvcm9qj/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_50kb.cool" 2021-08-26 12:16:32,760 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:16:32,764 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt 2021-08-26 12:16:32,771 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-26 12:16:32,772 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_5kb.cool 2021-08-26 12:16:32,772 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt 2021-08-26 12:16:32,772 INFO AddWeight Chromosome: chr1 2021-08-26 12:16:32,772 INFO AddWeight Resolution [bp]: 5000 2021-08-26 12:16:32,860 INFO AddWeight AddWeight successfully finished 2021-08-26 12:16:32,860 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_10kb.cool 2021-08-26 12:16:32,860 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt 2021-08-26 12:16:32,860 INFO AddWeight Chromosome: chr1 2021-08-26 12:16:32,860 INFO AddWeight Resolution [bp]: 10000 2021-08-26 12:16:32,929 INFO AddWeight AddWeight successfully finished 2021-08-26 12:16:32,929 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_20kb.cool 2021-08-26 12:16:32,929 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt 2021-08-26 12:16:32,929 INFO AddWeight Chromosome: chr1 2021-08-26 12:16:32,929 INFO AddWeight Resolution [bp]: 20000 2021-08-26 12:16:32,972 INFO AddWeight AddWeight successfully finished 2021-08-26 12:16:32,972 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_25kb.cool 2021-08-26 12:16:32,972 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt 2021-08-26 12:16:32,972 INFO AddWeight Chromosome: chr1 2021-08-26 12:16:32,972 INFO AddWeight Resolution [bp]: 25000 2021-08-26 12:16:33,007 INFO AddWeight AddWeight successfully finished 2021-08-26 12:16:33,007 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_50kb.cool 2021-08-26 12:16:33,007 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt 2021-08-26 12:16:33,008 INFO AddWeight Chromosome: chr1 2021-08-26 12:16:33,008 INFO AddWeight Resolution [bp]: 50000 2021-08-26 12:16:33,032 INFO AddWeight AddWeight successfully finished 2021-08-26 12:16:33,034 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.hic 2021-08-26 12:16:33,034 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_norm.hic 2021-08-26 12:16:33,034 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt 2021-08-26 12:16:33,034 INFO Vector2HiC Threads: 10 2021-08-26 12:16:33,064 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.hic" "/tmp/tmp727a1py8/inter.hic" 2021-08-26 12:16:33,317 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 12:16:33,317 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-08-26 12:16:33,318 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp727a1py8/inter.hic" "/tmp/tmp727a1py8/vector.txt" 2021-08-26 12:16:37,864 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-26 12:16:37,865 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-08-26 12:16:37,866 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp727a1py8/inter.hic" "/tmp/tmp727a1py8/vector.txt" 2021-08-26 12:16:41,728 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-26 12:16:41,728 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-08-26 12:16:41,745 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp727a1py8/inter.hic" "/tmp/tmp727a1py8/vector.txt" 2021-08-26 12:16:45,233 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-26 12:16:45,233 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-08-26 12:16:45,234 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp727a1py8/inter.hic" "/tmp/tmp727a1py8/vector.txt" 2021-08-26 12:16:48,943 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-26 12:16:48,943 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-08-26 12:16:48,944 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp727a1py8/inter.hic" "/tmp/tmp727a1py8/vector.txt" 2021-08-26 12:16:52,659 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-26 12:16:52,660 DEBUG SimpleSubprocess cp "/tmp/tmp727a1py8/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_norm.hic" 2021-08-26 12:16:52,968 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 12:16:53,022 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/merged_nodups.txt" 2021-08-26 12:17:09,472 INFO SimpleSubprocess CopyResult - 0:00:16 2021-08-26 12:17:09,472 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter.pairs.txt" 2021-08-26 12:17:17,628 INFO SimpleSubprocess CopyResult - 0:00:08 2021-08-26 12:17:17,628 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/vector.txt" 2021-08-26 12:17:17,637 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:17,638 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter.hic" 2021-08-26 12:17:20,268 INFO SimpleSubprocess CopyResult - 0:00:02 2021-08-26 12:17:20,268 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_statistics.txt" 2021-08-26 12:17:20,277 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:20,277 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_no_balanced_5kb.cool" 2021-08-26 12:17:20,435 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:20,435 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_5kb.cool" 2021-08-26 12:17:20,551 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:20,551 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_no_balanced_10kb.cool" 2021-08-26 12:17:20,679 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:20,679 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_10kb.cool" 2021-08-26 12:17:20,830 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:20,831 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_no_balanced_20kb.cool" 2021-08-26 12:17:20,907 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:20,907 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_20kb.cool" 2021-08-26 12:17:20,984 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:20,984 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_no_balanced_25kb.cool" 2021-08-26 12:17:21,087 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:21,087 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_25kb.cool" 2021-08-26 12:17:21,155 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:21,156 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_no_balanced_50kb.cool" 2021-08-26 12:17:21,223 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:21,223 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/inter_50kb.cool" 2021-08-26 12:17:21,311 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 12:17:21,451 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500316/__temp__" 2021-08-26 12:17:32,649 INFO SimpleSubprocess RemoveTemp - 0:00:11 2021-08-26 12:17:32,649 INFO BenchmarkPipeline 'SRR7500316' FINISHED, SUMMARY TIME - 7:26:13