2021-08-26 12:17:32,689 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179588' --- 2021-08-26 12:17:32,689 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179588.sra 2021-08-26 12:17:32,689 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__ 2021-08-26 12:17:32,689 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp5e6nnh0c "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179588.sra" 2021-08-26 12:58:18,250 INFO SimpleSubprocess Sra2FastQ - 0:40:45 2021-08-26 12:58:18,261 DEBUG SimpleSubprocess gzip /tmp/tmp5e6nnh0c/* 2021-08-26 15:58:41,427 INFO SimpleSubprocess GZipFastQ - 3:00:23 2021-08-26 15:58:41,464 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/fastq"; mv /tmp/tmp5e6nnh0c/SRR3179588_1.fastq.gz /tmp/tmp5e6nnh0c/SRR3179588_R1.fastq.gz; mv /tmp/tmp5e6nnh0c/SRR3179588_2.fastq.gz /tmp/tmp5e6nnh0c/SRR3179588_R2.fastq.gz; cp /tmp/tmp5e6nnh0c/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/fastq" 2021-08-26 16:04:19,362 INFO SimpleSubprocess CopyFiles - 0:05:37 2021-08-26 16:04:20,964 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__ 2021-08-26 16:04:20,964 INFO Juicer Genome assembly: mm10 2021-08-26 16:04:20,964 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-26 16:04:20,965 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 16:04:20,965 INFO Juicer Enzyme: DpnII 2021-08-26 16:04:20,965 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-26 16:04:20,965 INFO Juicer Threads: 10 2021-08-26 16:04:20,965 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/SRR3179588/__temp__" 2021-08-27 02:34:49,128 INFO SimpleSubprocess Juicer - 10:30:28 2021-08-27 02:34:49,152 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/SRR3179588/__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/SRR3179588/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/splits/SRR3179588_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/splits/SRR3179588_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/splits/SRR3179588.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/splits/SRR3179588.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 [2021-08-27T01:30:02,883] [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 [2021-08-27T02:04:14,253] [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/SRR3179588/__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 [2021-08-27T02:34:48,742] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__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/SRR3179588/__temp__/aligned for results 2021-08-27 02:34:49,154 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/merged_nodups.txt 2021-08-27 02:34:49,154 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt 2021-08-27 02:34:49,155 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp50xu5_zo/inter.pairs.txt" 2021-08-27 02:35:53,980 INFO SimpleSubprocess MakeInterPairs - 0:01:04 2021-08-27 02:35:53,980 DEBUG SimpleSubprocess cp "/tmp/tmp50xu5_zo/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt" 2021-08-27 02:35:55,590 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-27 02:35:56,222 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt 2021-08-27 02:35:56,223 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-27 02:35:56,223 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 02:35:56,223 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 02:35:56,223 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-27 02:35:56,223 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/SRR3179588/__temp__/aligned/inter.pairs.txt" "/tmp/tmpo2_cnx6y/inter_no_balanced.cool" 2021-08-27 02:37:31,360 INFO SimpleSubprocess MakeCool - 0:01:35 2021-08-27 02:37:31,361 DEBUG SimpleSubprocess cp "/tmp/tmpo2_cnx6y/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-27 02:37:31,392 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:37:31,396 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt 2021-08-27 02:37:31,396 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-27 02:37:31,396 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 02:37:31,396 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 02:37:31,396 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-27 02:37:31,397 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/SRR3179588/__temp__/aligned/inter.pairs.txt" "/tmp/tmpi6d5q14p/inter_no_balanced.cool" 2021-08-27 02:38:53,361 INFO SimpleSubprocess MakeCool - 0:01:21 2021-08-27 02:38:53,361 DEBUG SimpleSubprocess cp "/tmp/tmpi6d5q14p/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-27 02:38:53,389 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:38:53,392 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt 2021-08-27 02:38:53,392 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-27 02:38:53,392 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 02:38:53,393 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 02:38:53,393 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-27 02:38:53,393 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/SRR3179588/__temp__/aligned/inter.pairs.txt" "/tmp/tmpi1qv3ftm/inter_no_balanced.cool" 2021-08-27 02:40:12,046 INFO SimpleSubprocess MakeCool - 0:01:18 2021-08-27 02:40:12,046 DEBUG SimpleSubprocess cp "/tmp/tmpi1qv3ftm/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-27 02:40:12,069 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:40:12,072 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt 2021-08-27 02:40:12,072 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-27 02:40:12,072 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 02:40:12,072 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 02:40:12,072 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-27 02:40:12,072 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/SRR3179588/__temp__/aligned/inter.pairs.txt" "/tmp/tmpi9wf7tcx/inter_no_balanced.cool" 2021-08-27 02:41:29,633 INFO SimpleSubprocess MakeCool - 0:01:17 2021-08-27 02:41:29,633 DEBUG SimpleSubprocess cp "/tmp/tmpi9wf7tcx/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-27 02:41:29,654 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:41:29,656 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt 2021-08-27 02:41:29,657 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-27 02:41:29,657 INFO Pairs2Cool Genome assembly: mm10 2021-08-27 02:41:29,657 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 02:41:29,657 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-27 02:41:29,657 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/SRR3179588/__temp__/aligned/inter.pairs.txt" "/tmp/tmp3k72487c/inter_no_balanced.cool" 2021-08-27 02:42:41,534 INFO SimpleSubprocess MakeCool - 0:01:11 2021-08-27 02:42:41,534 DEBUG SimpleSubprocess cp "/tmp/tmp3k72487c/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-27 02:42:41,552 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:42:41,556 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-27 02:42:41,556 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_5kb.cool 2021-08-27 02:42:41,556 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 02:42:41,556 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpod0elqn7/inter.cool" 2021-08-27 02:42:41,585 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 02:42:41,586 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpod0elqn7/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 02:42:47,348 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-08-27 02:42:47,349 DEBUG SimpleSubprocess cp "/tmp/tmpod0elqn7/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_5kb.cool" 2021-08-27 02:42:47,381 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:42:47,385 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-27 02:42:47,386 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_10kb.cool 2021-08-27 02:42:47,386 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 02:42:47,386 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp5mm5aw59/inter.cool" 2021-08-27 02:42:47,413 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 02:42:47,413 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp5mm5aw59/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 02:42:50,440 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-27 02:42:50,441 DEBUG SimpleSubprocess cp "/tmp/tmp5mm5aw59/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_10kb.cool" 2021-08-27 02:42:50,468 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:42:50,471 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-27 02:42:50,471 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_20kb.cool 2021-08-27 02:42:50,471 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 02:42:50,472 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpwdh12p5f/inter.cool" 2021-08-27 02:42:50,495 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 02:42:50,495 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpwdh12p5f/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 02:42:52,694 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-27 02:42:52,694 DEBUG SimpleSubprocess cp "/tmp/tmpwdh12p5f/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_20kb.cool" 2021-08-27 02:42:52,736 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:42:52,739 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-27 02:42:52,739 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_25kb.cool 2021-08-27 02:42:52,739 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 02:42:52,739 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp7k7jf8pp/inter.cool" 2021-08-27 02:42:52,761 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 02:42:52,762 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp7k7jf8pp/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 02:42:54,710 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-27 02:42:54,711 DEBUG SimpleSubprocess cp "/tmp/tmp7k7jf8pp/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_25kb.cool" 2021-08-27 02:42:54,733 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:42:54,735 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-27 02:42:54,736 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_50kb.cool 2021-08-27 02:42:54,736 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-27 02:42:54,736 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpp9h4cgdj/inter.cool" 2021-08-27 02:42:54,755 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 02:42:54,755 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpp9h4cgdj/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-27 02:42:56,146 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-27 02:42:56,146 DEBUG SimpleSubprocess cp "/tmp/tmpp9h4cgdj/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_50kb.cool" 2021-08-27 02:42:56,165 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:42:56,169 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt 2021-08-27 02:42:56,175 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-27 02:42:56,176 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_5kb.cool 2021-08-27 02:42:56,176 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt 2021-08-27 02:42:56,176 INFO AddWeight Chromosome: chr11 2021-08-27 02:42:56,176 INFO AddWeight Resolution [bp]: 5000 2021-08-27 02:42:56,273 INFO AddWeight AddWeight successfully finished 2021-08-27 02:42:56,273 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_10kb.cool 2021-08-27 02:42:56,274 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt 2021-08-27 02:42:56,274 INFO AddWeight Chromosome: chr11 2021-08-27 02:42:56,274 INFO AddWeight Resolution [bp]: 10000 2021-08-27 02:42:56,328 INFO AddWeight AddWeight successfully finished 2021-08-27 02:42:56,328 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_20kb.cool 2021-08-27 02:42:56,328 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt 2021-08-27 02:42:56,328 INFO AddWeight Chromosome: chr11 2021-08-27 02:42:56,328 INFO AddWeight Resolution [bp]: 20000 2021-08-27 02:42:56,362 INFO AddWeight AddWeight successfully finished 2021-08-27 02:42:56,363 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_25kb.cool 2021-08-27 02:42:56,363 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt 2021-08-27 02:42:56,363 INFO AddWeight Chromosome: chr11 2021-08-27 02:42:56,363 INFO AddWeight Resolution [bp]: 25000 2021-08-27 02:42:56,393 INFO AddWeight AddWeight successfully finished 2021-08-27 02:42:56,393 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_50kb.cool 2021-08-27 02:42:56,393 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt 2021-08-27 02:42:56,393 INFO AddWeight Chromosome: chr11 2021-08-27 02:42:56,393 INFO AddWeight Resolution [bp]: 50000 2021-08-27 02:42:56,416 INFO AddWeight AddWeight successfully finished 2021-08-27 02:42:56,418 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.hic 2021-08-27 02:42:56,418 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_norm.hic 2021-08-27 02:42:56,418 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt 2021-08-27 02:42:56,419 INFO Vector2HiC Threads: 10 2021-08-27 02:42:56,440 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.hic" "/tmp/tmp7ptsa1is/inter.hic" 2021-08-27 02:42:56,754 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-27 02:42:56,754 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-08-27 02:42:56,755 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp7ptsa1is/inter.hic" "/tmp/tmp7ptsa1is/vector.txt" 2021-08-27 02:43:01,390 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-27 02:43:01,390 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-08-27 02:43:01,391 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp7ptsa1is/inter.hic" "/tmp/tmp7ptsa1is/vector.txt" 2021-08-27 02:43:05,819 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-27 02:43:05,819 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-08-27 02:43:05,971 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp7ptsa1is/inter.hic" "/tmp/tmp7ptsa1is/vector.txt" 2021-08-27 02:43:10,457 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-27 02:43:10,457 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-08-27 02:43:10,583 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp7ptsa1is/inter.hic" "/tmp/tmp7ptsa1is/vector.txt" 2021-08-27 02:43:14,667 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-27 02:43:14,667 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-08-27 02:43:14,667 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp7ptsa1is/inter.hic" "/tmp/tmp7ptsa1is/vector.txt" 2021-08-27 02:43:18,632 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-27 02:43:18,632 DEBUG SimpleSubprocess cp "/tmp/tmp7ptsa1is/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_norm.hic" 2021-08-27 02:43:18,989 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-27 02:43:19,665 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/merged_nodups.txt" 2021-08-27 02:45:00,783 INFO SimpleSubprocess CopyResult - 0:01:41 2021-08-27 02:45:00,783 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter.pairs.txt" 2021-08-27 02:45:14,022 INFO SimpleSubprocess CopyResult - 0:00:13 2021-08-27 02:45:14,023 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/vector.txt" 2021-08-27 02:45:14,196 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:14,196 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter.hic" 2021-08-27 02:45:19,634 INFO SimpleSubprocess CopyResult - 0:00:05 2021-08-27 02:45:19,634 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_statistics.txt" 2021-08-27 02:45:19,643 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:19,643 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_no_balanced_5kb.cool" 2021-08-27 02:45:19,931 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:19,931 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_5kb.cool" 2021-08-27 02:45:20,111 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:20,111 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_no_balanced_10kb.cool" 2021-08-27 02:45:20,363 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:20,364 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_10kb.cool" 2021-08-27 02:45:20,520 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:20,520 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_no_balanced_20kb.cool" 2021-08-27 02:45:20,639 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:20,639 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_20kb.cool" 2021-08-27 02:45:20,946 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:20,947 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_no_balanced_25kb.cool" 2021-08-27 02:45:21,113 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:21,113 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_25kb.cool" 2021-08-27 02:45:21,314 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:21,314 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_no_balanced_50kb.cool" 2021-08-27 02:45:21,809 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:21,809 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/inter_50kb.cool" 2021-08-27 02:45:22,380 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-27 02:45:22,484 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__" 2021-08-27 02:45:37,060 INFO SimpleSubprocess RemoveTemp - 0:00:14 2021-08-27 02:45:37,060 INFO BenchmarkPipeline 'SRR3179588' FINISHED, SUMMARY TIME - 14:28:04 2021-09-01 12:23:13,243 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179588' --- 2021-09-01 12:23:13,255 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__" 2021-09-01 12:23:13,264 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,265 INFO BenchmarkPipeline 'SRR3179588' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,773 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179588' --- 2021-09-02 13:38:17,773 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179588/__temp__" 2021-09-02 13:38:17,781 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,782 INFO BenchmarkPipeline 'SRR3179588' FINISHED, SUMMARY TIME - 0:00:00