2021-09-04 00:24:27,670 INFO BenchmarkPipeline --- START PROCESSING 'SRR5855104-SRR5855105' --- 2021-09-04 00:24:27,670 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855104.sra 2021-09-04 00:24:27,670 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__ 2021-09-04 00:24:27,671 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp29t0vart "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855104.sra" 2021-09-04 00:32:50,309 INFO SimpleSubprocess Sra2FastQ - 0:08:22 2021-09-04 00:32:50,310 DEBUG SimpleSubprocess gzip /tmp/tmp29t0vart/* 2021-09-04 00:52:35,021 INFO SimpleSubprocess GZipFastQ - 0:19:44 2021-09-04 00:52:35,021 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/fastq"; mv /tmp/tmp29t0vart/SRR5855104_1.fastq.gz /tmp/tmp29t0vart/SRR5855104_R1.fastq.gz; mv /tmp/tmp29t0vart/SRR5855104_2.fastq.gz /tmp/tmp29t0vart/SRR5855104_R2.fastq.gz; cp /tmp/tmp29t0vart/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/fastq" 2021-09-04 00:52:38,773 INFO SimpleSubprocess CopyFiles - 0:00:03 2021-09-04 00:52:39,263 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855105.sra 2021-09-04 00:52:39,263 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__ 2021-09-04 00:52:39,264 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpthhivk3e "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855105.sra" 2021-09-04 00:59:59,879 INFO SimpleSubprocess Sra2FastQ - 0:07:20 2021-09-04 00:59:59,879 DEBUG SimpleSubprocess gzip /tmp/tmpthhivk3e/* 2021-09-04 01:16:59,517 INFO SimpleSubprocess GZipFastQ - 0:16:59 2021-09-04 01:16:59,517 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/fastq"; mv /tmp/tmpthhivk3e/SRR5855105_2.fastq.gz /tmp/tmpthhivk3e/SRR5855105_R2.fastq.gz; mv /tmp/tmpthhivk3e/SRR5855105_1.fastq.gz /tmp/tmpthhivk3e/SRR5855105_R1.fastq.gz; cp /tmp/tmpthhivk3e/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/fastq" 2021-09-04 01:17:02,657 INFO SimpleSubprocess CopyFiles - 0:00:03 2021-09-04 01:17:03,089 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__ 2021-09-04 01:17:03,090 INFO Juicer Genome assembly: mm10 2021-09-04 01:17:03,090 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-04 01:17:03,090 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 01:17:03,090 INFO Juicer Enzyme: DpnII 2021-09-04 01:17:03,090 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-04 01:17:03,090 INFO Juicer Threads: 10 2021-09-04 01:17:03,090 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits" 2021-09-04 01:17:03,099 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-04 01:17:03,100 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/SRR5855104-SRR5855105/__temp__" 2021-09-04 06:45:41,206 INFO SimpleSubprocess Juicer - 5:28:38 2021-09-04 06:45:41,215 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/SRR5855104-SRR5855105/__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/SRR5855104-SRR5855105/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855104_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855104_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855104.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855104.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855105_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855105_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855105.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/splits/SRR5855105.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 [2021-09-04T04:42:26,888] [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 [2021-09-04T05:52:34,202] [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/SRR5855104-SRR5855105/__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 [2021-09-04T06:45:40,711] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__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/SRR5855104-SRR5855105/__temp__/aligned for results 2021-09-04 06:45:41,233 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/merged_nodups.txt 2021-09-04 06:45:41,233 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt 2021-09-04 06:45:41,233 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpjrjqbqqn/inter.pairs.txt" 2021-09-04 06:47:05,645 INFO SimpleSubprocess MakeInterPairs - 0:01:24 2021-09-04 06:47:05,645 DEBUG SimpleSubprocess cp "/tmp/tmpjrjqbqqn/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt" 2021-09-04 06:47:07,968 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-04 06:47:08,293 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt 2021-09-04 06:47:08,293 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-04 06:47:08,293 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 06:47:08,293 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 06:47:08,293 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-04 06:47:08,294 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/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt" "/tmp/tmpicl3qc5t/inter_no_balanced.cool" 2021-09-04 06:50:37,320 INFO SimpleSubprocess MakeCool - 0:03:29 2021-09-04 06:50:37,321 DEBUG SimpleSubprocess cp "/tmp/tmpicl3qc5t/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-04 06:50:37,430 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 06:50:37,445 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt 2021-09-04 06:50:37,445 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-04 06:50:37,445 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 06:50:37,446 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 06:50:37,446 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-04 06:50:37,446 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/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt" "/tmp/tmp21i6anwi/inter_no_balanced.cool" 2021-09-04 06:53:48,878 INFO SimpleSubprocess MakeCool - 0:03:11 2021-09-04 06:53:48,879 DEBUG SimpleSubprocess cp "/tmp/tmp21i6anwi/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-04 06:53:48,973 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 06:53:48,986 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt 2021-09-04 06:53:48,986 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-04 06:53:48,986 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 06:53:48,986 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 06:53:48,987 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-04 06:53:48,987 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/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt" "/tmp/tmpb26jss49/inter_no_balanced.cool" 2021-09-04 06:56:46,314 INFO SimpleSubprocess MakeCool - 0:02:57 2021-09-04 06:56:46,314 DEBUG SimpleSubprocess cp "/tmp/tmpb26jss49/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-04 06:56:46,401 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 06:56:46,413 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt 2021-09-04 06:56:46,413 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-04 06:56:46,413 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 06:56:46,413 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 06:56:46,413 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-04 06:56:46,413 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/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt" "/tmp/tmpxuabc3zo/inter_no_balanced.cool" 2021-09-04 06:59:38,953 INFO SimpleSubprocess MakeCool - 0:02:52 2021-09-04 06:59:38,953 DEBUG SimpleSubprocess cp "/tmp/tmpxuabc3zo/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-04 06:59:39,027 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 06:59:39,037 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt 2021-09-04 06:59:39,038 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-04 06:59:39,038 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 06:59:39,038 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 06:59:39,038 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-04 06:59:39,038 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/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2t2ml5le/inter_no_balanced.cool" 2021-09-04 07:02:18,240 INFO SimpleSubprocess MakeCool - 0:02:39 2021-09-04 07:02:18,240 DEBUG SimpleSubprocess cp "/tmp/tmp2t2ml5le/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-04 07:02:18,306 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 07:02:18,317 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-04 07:02:18,317 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_5kb.cool 2021-09-04 07:02:18,317 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 07:02:18,317 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp__2tqg7g/inter.cool" 2021-09-04 07:02:18,434 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 07:02:18,434 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp__2tqg7g/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 07:02:32,535 INFO SimpleSubprocess NormalizeCool - 0:00:14 2021-09-04 07:02:32,535 DEBUG SimpleSubprocess cp "/tmp/tmp__2tqg7g/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_5kb.cool" 2021-09-04 07:02:32,644 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 07:02:32,661 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-04 07:02:32,661 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_10kb.cool 2021-09-04 07:02:32,661 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 07:02:32,661 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp96xat5x0/inter.cool" 2021-09-04 07:02:32,757 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 07:02:32,757 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp96xat5x0/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 07:02:48,793 INFO SimpleSubprocess NormalizeCool - 0:00:16 2021-09-04 07:02:48,793 DEBUG SimpleSubprocess cp "/tmp/tmp96xat5x0/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_10kb.cool" 2021-09-04 07:02:48,887 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 07:02:48,902 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-04 07:02:48,902 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_20kb.cool 2021-09-04 07:02:48,902 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 07:02:48,903 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpzx00kf6e/inter.cool" 2021-09-04 07:02:48,984 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 07:02:48,984 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpzx00kf6e/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 07:03:01,605 INFO SimpleSubprocess NormalizeCool - 0:00:12 2021-09-04 07:03:01,605 DEBUG SimpleSubprocess cp "/tmp/tmpzx00kf6e/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_20kb.cool" 2021-09-04 07:03:01,687 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 07:03:01,699 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-04 07:03:01,700 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_25kb.cool 2021-09-04 07:03:01,700 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 07:03:01,700 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpv1mvlhol/inter.cool" 2021-09-04 07:03:01,773 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 07:03:01,774 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpv1mvlhol/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 07:03:13,231 INFO SimpleSubprocess NormalizeCool - 0:00:11 2021-09-04 07:03:13,231 DEBUG SimpleSubprocess cp "/tmp/tmpv1mvlhol/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_25kb.cool" 2021-09-04 07:03:13,305 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 07:03:13,316 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-04 07:03:13,317 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_50kb.cool 2021-09-04 07:03:13,317 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 07:03:13,317 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp4kkgf0uw/inter.cool" 2021-09-04 07:03:13,378 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 07:03:13,379 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp4kkgf0uw/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 07:03:22,052 INFO SimpleSubprocess NormalizeCool - 0:00:08 2021-09-04 07:03:22,053 DEBUG SimpleSubprocess cp "/tmp/tmp4kkgf0uw/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_50kb.cool" 2021-09-04 07:03:22,114 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 07:03:22,124 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt 2021-09-04 07:03:22,132 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-04 07:03:22,133 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_5kb.cool 2021-09-04 07:03:22,133 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt 2021-09-04 07:03:22,133 INFO AddWeight Chromosome: chr2 2021-09-04 07:03:22,133 INFO AddWeight Resolution [bp]: 5000 2021-09-04 07:03:22,248 INFO AddWeight AddWeight successfully finished 2021-09-04 07:03:22,248 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_10kb.cool 2021-09-04 07:03:22,248 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt 2021-09-04 07:03:22,249 INFO AddWeight Chromosome: chr2 2021-09-04 07:03:22,249 INFO AddWeight Resolution [bp]: 10000 2021-09-04 07:03:22,293 INFO AddWeight AddWeight successfully finished 2021-09-04 07:03:22,293 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_20kb.cool 2021-09-04 07:03:22,293 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt 2021-09-04 07:03:22,293 INFO AddWeight Chromosome: chr2 2021-09-04 07:03:22,294 INFO AddWeight Resolution [bp]: 20000 2021-09-04 07:03:22,323 INFO AddWeight AddWeight successfully finished 2021-09-04 07:03:22,323 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_25kb.cool 2021-09-04 07:03:22,323 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt 2021-09-04 07:03:22,323 INFO AddWeight Chromosome: chr2 2021-09-04 07:03:22,323 INFO AddWeight Resolution [bp]: 25000 2021-09-04 07:03:22,349 INFO AddWeight AddWeight successfully finished 2021-09-04 07:03:22,349 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_50kb.cool 2021-09-04 07:03:22,349 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt 2021-09-04 07:03:22,349 INFO AddWeight Chromosome: chr2 2021-09-04 07:03:22,349 INFO AddWeight Resolution [bp]: 50000 2021-09-04 07:03:22,369 INFO AddWeight AddWeight successfully finished 2021-09-04 07:03:22,371 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.hic 2021-09-04 07:03:22,371 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_norm.hic 2021-09-04 07:03:22,371 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt 2021-09-04 07:03:22,371 INFO Vector2HiC Threads: 10 2021-09-04 07:03:22,398 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.hic" "/tmp/tmpflfnit9l/inter.hic" 2021-09-04 07:03:23,147 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 07:03:23,147 INFO Vector2HiC Vector: vector c-tale_normalization chr2 5000 BP 2021-09-04 07:03:23,149 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpflfnit9l/inter.hic" "/tmp/tmpflfnit9l/vector.txt" 2021-09-04 07:03:27,756 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-04 07:03:27,756 INFO Vector2HiC Vector: vector c-tale_normalization chr2 10000 BP 2021-09-04 07:03:27,757 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpflfnit9l/inter.hic" "/tmp/tmpflfnit9l/vector.txt" 2021-09-04 07:03:31,756 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-04 07:03:31,757 INFO Vector2HiC Vector: vector c-tale_normalization chr2 20000 BP 2021-09-04 07:03:31,757 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpflfnit9l/inter.hic" "/tmp/tmpflfnit9l/vector.txt" 2021-09-04 07:03:35,247 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-04 07:03:35,247 INFO Vector2HiC Vector: vector c-tale_normalization chr2 25000 BP 2021-09-04 07:03:35,248 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpflfnit9l/inter.hic" "/tmp/tmpflfnit9l/vector.txt" 2021-09-04 07:03:39,064 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-04 07:03:39,064 INFO Vector2HiC Vector: vector c-tale_normalization chr2 50000 BP 2021-09-04 07:03:39,083 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpflfnit9l/inter.hic" "/tmp/tmpflfnit9l/vector.txt" 2021-09-04 07:03:42,815 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-04 07:03:42,815 DEBUG SimpleSubprocess cp "/tmp/tmpflfnit9l/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_norm.hic" 2021-09-04 07:03:43,614 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 07:03:43,748 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/merged_nodups.txt" 2021-09-04 07:04:54,191 INFO SimpleSubprocess CopyResult - 0:01:10 2021-09-04 07:04:54,191 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter.pairs.txt" 2021-09-04 07:05:10,757 INFO SimpleSubprocess CopyResult - 0:00:16 2021-09-04 07:05:10,770 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/vector.txt" 2021-09-04 07:05:10,826 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 07:05:10,826 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter.hic" 2021-09-04 07:05:27,690 INFO SimpleSubprocess CopyResult - 0:00:16 2021-09-04 07:05:27,690 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_statistics.txt" 2021-09-04 07:05:27,740 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 07:05:27,740 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_no_balanced_5kb.cool" 2021-09-04 07:05:29,573 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 07:05:29,574 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_5kb.cool" 2021-09-04 07:05:30,792 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 07:05:30,792 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_no_balanced_10kb.cool" 2021-09-04 07:05:32,189 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 07:05:32,189 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_10kb.cool" 2021-09-04 07:05:32,986 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 07:05:32,986 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_no_balanced_20kb.cool" 2021-09-04 07:05:34,176 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 07:05:34,176 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_20kb.cool" 2021-09-04 07:05:35,176 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 07:05:35,176 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_no_balanced_25kb.cool" 2021-09-04 07:05:35,946 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 07:05:35,946 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_25kb.cool" 2021-09-04 07:05:37,751 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 07:05:37,752 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_no_balanced_50kb.cool" 2021-09-04 07:05:38,340 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 07:05:38,340 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/inter_50kb.cool" 2021-09-04 07:05:39,417 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 07:05:39,518 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855104-SRR5855105/__temp__" 2021-09-04 07:05:45,590 INFO SimpleSubprocess RemoveTemp - 0:00:06 2021-09-04 07:05:45,590 INFO BenchmarkPipeline 'SRR5855104-SRR5855105' FINISHED, SUMMARY TIME - 6:41:17