2021-08-29 19:46:56,998 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099908' --- 2021-08-29 19:46:56,998 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099908.sra 2021-08-29 19:46:56,998 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__ 2021-08-29 19:46:56,999 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpp7ko6q7n "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099908.sra" 2021-08-29 20:19:17,877 INFO SimpleSubprocess Sra2FastQ - 0:32:20 2021-08-29 20:19:17,924 DEBUG SimpleSubprocess gzip /tmp/tmpp7ko6q7n/* 2021-08-29 22:57:32,532 INFO SimpleSubprocess GZipFastQ - 2:38:14 2021-08-29 22:57:32,568 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/fastq"; mv /tmp/tmpp7ko6q7n/SRR5099908_1.fastq.gz /tmp/tmpp7ko6q7n/SRR5099908_R1.fastq.gz; mv /tmp/tmpp7ko6q7n/SRR5099908_2.fastq.gz /tmp/tmpp7ko6q7n/SRR5099908_R2.fastq.gz; cp /tmp/tmpp7ko6q7n/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/fastq" 2021-08-29 23:02:09,854 INFO SimpleSubprocess CopyFiles - 0:04:37 2021-08-29 23:02:11,763 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__ 2021-08-29 23:02:11,764 INFO Juicer Genome assembly: mm10 2021-08-29 23:02:11,764 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-29 23:02:11,764 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 23:02:11,764 INFO Juicer Enzyme: DpnII 2021-08-29 23:02:11,764 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-29 23:02:11,764 INFO Juicer Threads: 10 2021-08-29 23:02:11,764 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/SRR5099908/__temp__" 2021-08-30 08:25:36,109 INFO SimpleSubprocess Juicer - 9:23:24 2021-08-30 08:25:36,134 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/SRR5099908/__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/SRR5099908/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/splits/SRR5099908_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/splits/SRR5099908_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/splits/SRR5099908.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/splits/SRR5099908.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 [2021-08-30T06:18:31,679] [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 [2021-08-30T06:54:38,355] [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/SRR5099908/__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 [2021-08-30T08:25:35,778] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__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/SRR5099908/__temp__/aligned for results 2021-08-30 08:25:36,141 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/merged_nodups.txt 2021-08-30 08:25:36,141 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt 2021-08-30 08:25:36,141 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp8fz7w_jp/inter.pairs.txt" 2021-08-30 08:26:41,996 INFO SimpleSubprocess MakeInterPairs - 0:01:05 2021-08-30 08:26:41,996 DEBUG SimpleSubprocess cp "/tmp/tmp8fz7w_jp/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt" 2021-08-30 08:26:43,632 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-30 08:26:43,873 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt 2021-08-30 08:26:43,873 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-30 08:26:43,873 INFO Pairs2Cool Genome assembly: mm10 2021-08-30 08:26:43,873 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-30 08:26:43,873 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-30 08:26:43,899 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/SRR5099908/__temp__/aligned/inter.pairs.txt" "/tmp/tmpkbwpfimk/inter_no_balanced.cool" 2021-08-30 08:28:11,194 INFO SimpleSubprocess MakeCool - 0:01:27 2021-08-30 08:28:11,194 DEBUG SimpleSubprocess cp "/tmp/tmpkbwpfimk/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-30 08:28:11,225 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:28:11,229 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt 2021-08-30 08:28:11,229 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-30 08:28:11,229 INFO Pairs2Cool Genome assembly: mm10 2021-08-30 08:28:11,230 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-30 08:28:11,230 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-30 08:28:11,258 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/SRR5099908/__temp__/aligned/inter.pairs.txt" "/tmp/tmpu44_y6q2/inter_no_balanced.cool" 2021-08-30 08:29:30,841 INFO SimpleSubprocess MakeCool - 0:01:19 2021-08-30 08:29:30,842 DEBUG SimpleSubprocess cp "/tmp/tmpu44_y6q2/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-30 08:29:30,868 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:29:30,871 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt 2021-08-30 08:29:30,871 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-30 08:29:30,871 INFO Pairs2Cool Genome assembly: mm10 2021-08-30 08:29:30,872 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-30 08:29:30,872 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-30 08:29:30,872 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/SRR5099908/__temp__/aligned/inter.pairs.txt" "/tmp/tmpb4dk_5m3/inter_no_balanced.cool" 2021-08-30 08:30:45,775 INFO SimpleSubprocess MakeCool - 0:01:14 2021-08-30 08:30:45,776 DEBUG SimpleSubprocess cp "/tmp/tmpb4dk_5m3/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-30 08:30:45,797 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:30:45,799 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt 2021-08-30 08:30:45,799 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-30 08:30:45,800 INFO Pairs2Cool Genome assembly: mm10 2021-08-30 08:30:45,800 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-30 08:30:45,800 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-30 08:30:45,800 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/SRR5099908/__temp__/aligned/inter.pairs.txt" "/tmp/tmp536845ph/inter_no_balanced.cool" 2021-08-30 08:31:58,286 INFO SimpleSubprocess MakeCool - 0:01:12 2021-08-30 08:31:58,286 DEBUG SimpleSubprocess cp "/tmp/tmp536845ph/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-30 08:31:58,307 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:31:58,309 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt 2021-08-30 08:31:58,310 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-30 08:31:58,310 INFO Pairs2Cool Genome assembly: mm10 2021-08-30 08:31:58,310 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-30 08:31:58,310 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-30 08:31:58,310 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/SRR5099908/__temp__/aligned/inter.pairs.txt" "/tmp/tmpz9bhqk3x/inter_no_balanced.cool" 2021-08-30 08:33:08,360 INFO SimpleSubprocess MakeCool - 0:01:10 2021-08-30 08:33:08,360 DEBUG SimpleSubprocess cp "/tmp/tmpz9bhqk3x/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-30 08:33:08,378 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:33:08,403 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-30 08:33:08,403 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_5kb.cool 2021-08-30 08:33:08,403 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-30 08:33:08,427 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpagdatj3q/inter.cool" 2021-08-30 08:33:08,456 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-30 08:33:08,456 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpagdatj3q/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-30 08:33:16,867 INFO SimpleSubprocess NormalizeCool - 0:00:08 2021-08-30 08:33:16,868 DEBUG SimpleSubprocess cp "/tmp/tmpagdatj3q/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_5kb.cool" 2021-08-30 08:33:16,897 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:33:16,929 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-30 08:33:16,929 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_10kb.cool 2021-08-30 08:33:16,929 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-30 08:33:16,930 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp402_auva/inter.cool" 2021-08-30 08:33:16,954 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-30 08:33:16,954 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp402_auva/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-30 08:33:21,335 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-08-30 08:33:21,335 DEBUG SimpleSubprocess cp "/tmp/tmp402_auva/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_10kb.cool" 2021-08-30 08:33:21,362 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:33:21,365 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-30 08:33:21,365 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_20kb.cool 2021-08-30 08:33:21,365 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-30 08:33:21,366 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpnn7f8vai/inter.cool" 2021-08-30 08:33:21,388 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-30 08:33:21,388 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpnn7f8vai/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-30 08:33:24,716 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-30 08:33:24,716 DEBUG SimpleSubprocess cp "/tmp/tmpnn7f8vai/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_20kb.cool" 2021-08-30 08:33:24,737 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:33:24,740 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-30 08:33:24,740 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_25kb.cool 2021-08-30 08:33:24,740 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-30 08:33:24,740 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpncelvwal/inter.cool" 2021-08-30 08:33:24,760 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-30 08:33:24,760 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpncelvwal/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-30 08:33:27,664 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-30 08:33:27,664 DEBUG SimpleSubprocess cp "/tmp/tmpncelvwal/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_25kb.cool" 2021-08-30 08:33:27,684 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:33:27,686 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-30 08:33:27,686 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_50kb.cool 2021-08-30 08:33:27,686 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-30 08:33:27,687 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpes8xctwf/inter.cool" 2021-08-30 08:33:27,704 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-30 08:33:27,704 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpes8xctwf/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-30 08:33:29,516 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-30 08:33:29,516 DEBUG SimpleSubprocess cp "/tmp/tmpes8xctwf/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_50kb.cool" 2021-08-30 08:33:29,533 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:33:29,537 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt 2021-08-30 08:33:29,543 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-30 08:33:29,543 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_5kb.cool 2021-08-30 08:33:29,544 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt 2021-08-30 08:33:29,544 INFO AddWeight Chromosome: chr1 2021-08-30 08:33:29,544 INFO AddWeight Resolution [bp]: 5000 2021-08-30 08:33:29,689 INFO AddWeight AddWeight successfully finished 2021-08-30 08:33:29,689 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_10kb.cool 2021-08-30 08:33:29,689 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt 2021-08-30 08:33:29,689 INFO AddWeight Chromosome: chr1 2021-08-30 08:33:29,690 INFO AddWeight Resolution [bp]: 10000 2021-08-30 08:33:29,759 INFO AddWeight AddWeight successfully finished 2021-08-30 08:33:29,759 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_20kb.cool 2021-08-30 08:33:29,759 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt 2021-08-30 08:33:29,759 INFO AddWeight Chromosome: chr1 2021-08-30 08:33:29,759 INFO AddWeight Resolution [bp]: 20000 2021-08-30 08:33:29,800 INFO AddWeight AddWeight successfully finished 2021-08-30 08:33:29,800 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_25kb.cool 2021-08-30 08:33:29,800 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt 2021-08-30 08:33:29,800 INFO AddWeight Chromosome: chr1 2021-08-30 08:33:29,801 INFO AddWeight Resolution [bp]: 25000 2021-08-30 08:33:29,835 INFO AddWeight AddWeight successfully finished 2021-08-30 08:33:29,836 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_50kb.cool 2021-08-30 08:33:29,836 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt 2021-08-30 08:33:29,836 INFO AddWeight Chromosome: chr1 2021-08-30 08:33:29,836 INFO AddWeight Resolution [bp]: 50000 2021-08-30 08:33:29,860 INFO AddWeight AddWeight successfully finished 2021-08-30 08:33:29,862 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.hic 2021-08-30 08:33:29,862 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_norm.hic 2021-08-30 08:33:29,862 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt 2021-08-30 08:33:29,862 INFO Vector2HiC Threads: 10 2021-08-30 08:33:29,895 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.hic" "/tmp/tmpzmaojsyx/inter.hic" 2021-08-30 08:33:30,176 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-30 08:33:30,176 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-08-30 08:33:30,178 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzmaojsyx/inter.hic" "/tmp/tmpzmaojsyx/vector.txt" 2021-08-30 08:33:35,559 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-08-30 08:33:35,559 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-08-30 08:33:35,561 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzmaojsyx/inter.hic" "/tmp/tmpzmaojsyx/vector.txt" 2021-08-30 08:33:39,871 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-30 08:33:39,871 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-08-30 08:33:39,872 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzmaojsyx/inter.hic" "/tmp/tmpzmaojsyx/vector.txt" 2021-08-30 08:33:43,554 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-30 08:33:43,554 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-08-30 08:33:43,555 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzmaojsyx/inter.hic" "/tmp/tmpzmaojsyx/vector.txt" 2021-08-30 08:33:47,658 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-30 08:33:47,658 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-08-30 08:33:47,678 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzmaojsyx/inter.hic" "/tmp/tmpzmaojsyx/vector.txt" 2021-08-30 08:33:51,833 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-30 08:33:51,833 DEBUG SimpleSubprocess cp "/tmp/tmpzmaojsyx/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_norm.hic" 2021-08-30 08:33:52,188 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-30 08:33:52,248 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/merged_nodups.txt" 2021-08-30 08:35:34,987 INFO SimpleSubprocess CopyResult - 0:01:42 2021-08-30 08:35:34,988 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter.pairs.txt" 2021-08-30 08:35:48,815 INFO SimpleSubprocess CopyResult - 0:00:13 2021-08-30 08:35:48,815 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/vector.txt" 2021-08-30 08:35:48,913 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:48,913 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter.hic" 2021-08-30 08:35:52,103 INFO SimpleSubprocess CopyResult - 0:00:03 2021-08-30 08:35:52,104 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_statistics.txt" 2021-08-30 08:35:52,112 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:52,112 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_no_balanced_5kb.cool" 2021-08-30 08:35:52,339 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:52,339 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_5kb.cool" 2021-08-30 08:35:52,548 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:52,548 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_no_balanced_10kb.cool" 2021-08-30 08:35:52,716 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:52,716 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_10kb.cool" 2021-08-30 08:35:52,884 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:52,884 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_no_balanced_20kb.cool" 2021-08-30 08:35:53,031 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:53,031 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_20kb.cool" 2021-08-30 08:35:53,127 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:53,127 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_no_balanced_25kb.cool" 2021-08-30 08:35:53,200 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:53,200 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_25kb.cool" 2021-08-30 08:35:53,268 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:53,268 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_no_balanced_50kb.cool" 2021-08-30 08:35:53,391 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:53,392 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/inter_50kb.cool" 2021-08-30 08:35:53,466 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-30 08:35:53,732 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__" 2021-08-30 08:36:13,238 INFO SimpleSubprocess RemoveTemp - 0:00:19 2021-08-30 08:36:13,239 INFO BenchmarkPipeline 'SRR5099908' FINISHED, SUMMARY TIME - 12:49:16 2021-09-01 12:23:13,415 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099908' --- 2021-09-01 12:23:13,416 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__" 2021-09-01 12:23:13,425 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,425 INFO BenchmarkPipeline 'SRR5099908' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,836 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099908' --- 2021-09-02 13:38:17,836 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099908/__temp__" 2021-09-02 13:38:17,844 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,845 INFO BenchmarkPipeline 'SRR5099908' FINISHED, SUMMARY TIME - 0:00:00