2021-09-03 08:00:30,185 INFO BenchmarkPipeline --- START PROCESSING 'SRR5855100-SRR5855101' --- 2021-09-03 08:00:30,185 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855100.sra 2021-09-03 08:00:30,185 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__ 2021-09-03 08:00:30,185 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp17v9n6bt "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855100.sra" 2021-09-03 08:08:39,375 INFO SimpleSubprocess Sra2FastQ - 0:08:09 2021-09-03 08:08:39,376 DEBUG SimpleSubprocess gzip /tmp/tmp17v9n6bt/* 2021-09-03 08:28:21,773 INFO SimpleSubprocess GZipFastQ - 0:19:42 2021-09-03 08:28:21,774 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/fastq"; mv /tmp/tmp17v9n6bt/SRR5855100_1.fastq.gz /tmp/tmp17v9n6bt/SRR5855100_R1.fastq.gz; mv /tmp/tmp17v9n6bt/SRR5855100_2.fastq.gz /tmp/tmp17v9n6bt/SRR5855100_R2.fastq.gz; cp /tmp/tmp17v9n6bt/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/fastq" 2021-09-03 08:28:25,518 INFO SimpleSubprocess CopyFiles - 0:00:03 2021-09-03 08:28:26,022 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855101.sra 2021-09-03 08:28:26,022 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__ 2021-09-03 08:28:26,022 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpafm4etic "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855101.sra" 2021-09-03 08:38:31,026 INFO SimpleSubprocess Sra2FastQ - 0:10:05 2021-09-03 08:38:31,026 DEBUG SimpleSubprocess gzip /tmp/tmpafm4etic/* 2021-09-03 09:02:09,697 INFO SimpleSubprocess GZipFastQ - 0:23:38 2021-09-03 09:02:09,698 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/fastq"; mv /tmp/tmpafm4etic/SRR5855101_1.fastq.gz /tmp/tmpafm4etic/SRR5855101_R1.fastq.gz; mv /tmp/tmpafm4etic/SRR5855101_2.fastq.gz /tmp/tmpafm4etic/SRR5855101_R2.fastq.gz; cp /tmp/tmpafm4etic/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/fastq" 2021-09-03 09:02:14,196 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-03 09:02:14,788 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__ 2021-09-03 09:02:14,788 INFO Juicer Genome assembly: mm10 2021-09-03 09:02:14,788 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-03 09:02:14,788 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 09:02:14,788 INFO Juicer Enzyme: DpnII 2021-09-03 09:02:14,788 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-03 09:02:14,788 INFO Juicer Threads: 10 2021-09-03 09:02:14,788 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits" 2021-09-03 09:02:14,798 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-03 09:02:14,798 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/SRR5855100-SRR5855101/__temp__" 2021-09-03 15:35:33,883 INFO SimpleSubprocess Juicer - 6:33:19 2021-09-03 15:35:33,902 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/SRR5855100-SRR5855101/__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/SRR5855100-SRR5855101/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855100_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855100_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855100.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855100.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855101_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855101_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855101.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/splits/SRR5855101.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 [2021-09-03T13:07:26,893] [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 [2021-09-03T14:31:32,142] [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/SRR5855100-SRR5855101/__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 [2021-09-03T15:35:33,552] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__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/SRR5855100-SRR5855101/__temp__/aligned for results 2021-09-03 15:35:33,904 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/merged_nodups.txt 2021-09-03 15:35:33,904 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt 2021-09-03 15:35:33,904 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpwfh1iulr/inter.pairs.txt" 2021-09-03 15:37:13,681 INFO SimpleSubprocess MakeInterPairs - 0:01:39 2021-09-03 15:37:13,682 DEBUG SimpleSubprocess cp "/tmp/tmpwfh1iulr/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt" 2021-09-03 15:37:16,351 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-03 15:37:16,773 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt 2021-09-03 15:37:16,773 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-03 15:37:16,773 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 15:37:16,773 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 15:37:16,773 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-03 15:37:16,773 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/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt" "/tmp/tmpg4qix47x/inter_no_balanced.cool" 2021-09-03 15:41:21,428 INFO SimpleSubprocess MakeCool - 0:04:04 2021-09-03 15:41:21,428 DEBUG SimpleSubprocess cp "/tmp/tmpg4qix47x/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-03 15:41:21,576 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:41:21,593 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt 2021-09-03 15:41:21,593 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-03 15:41:21,593 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 15:41:21,593 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 15:41:21,593 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-03 15:41:21,593 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/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt" "/tmp/tmpq6u7b6o2/inter_no_balanced.cool" 2021-09-03 15:45:08,993 INFO SimpleSubprocess MakeCool - 0:03:47 2021-09-03 15:45:08,993 DEBUG SimpleSubprocess cp "/tmp/tmpq6u7b6o2/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-03 15:45:09,107 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:45:09,125 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt 2021-09-03 15:45:09,125 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-03 15:45:09,125 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 15:45:09,125 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 15:45:09,126 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-03 15:45:09,126 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/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt" "/tmp/tmpagy6ob9j/inter_no_balanced.cool" 2021-09-03 15:48:36,239 INFO SimpleSubprocess MakeCool - 0:03:27 2021-09-03 15:48:36,239 DEBUG SimpleSubprocess cp "/tmp/tmpagy6ob9j/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-03 15:48:36,332 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:48:36,346 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt 2021-09-03 15:48:36,346 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-03 15:48:36,346 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 15:48:36,346 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 15:48:36,346 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-03 15:48:36,346 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/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt" "/tmp/tmpq3o6xunh/inter_no_balanced.cool" 2021-09-03 15:51:59,598 INFO SimpleSubprocess MakeCool - 0:03:23 2021-09-03 15:51:59,598 DEBUG SimpleSubprocess cp "/tmp/tmpq3o6xunh/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-03 15:51:59,691 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:51:59,705 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt 2021-09-03 15:51:59,705 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-03 15:51:59,705 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 15:51:59,705 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 15:51:59,705 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-03 15:51:59,706 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/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt" "/tmp/tmpbvz3phcz/inter_no_balanced.cool" 2021-09-03 15:55:08,057 INFO SimpleSubprocess MakeCool - 0:03:08 2021-09-03 15:55:08,057 DEBUG SimpleSubprocess cp "/tmp/tmpbvz3phcz/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-03 15:55:08,133 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:55:08,145 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-03 15:55:08,145 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_5kb.cool 2021-09-03 15:55:08,145 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 15:55:08,145 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpnrgwz6zl/inter.cool" 2021-09-03 15:55:08,281 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 15:55:08,281 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpnrgwz6zl/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 15:55:24,392 INFO SimpleSubprocess NormalizeCool - 0:00:16 2021-09-03 15:55:24,392 DEBUG SimpleSubprocess cp "/tmp/tmpnrgwz6zl/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_5kb.cool" 2021-09-03 15:55:24,523 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:55:24,543 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-03 15:55:24,543 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_10kb.cool 2021-09-03 15:55:24,543 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 15:55:24,544 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpxdxfll9l/inter.cool" 2021-09-03 15:55:24,654 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 15:55:24,654 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpxdxfll9l/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 15:55:43,172 INFO SimpleSubprocess NormalizeCool - 0:00:18 2021-09-03 15:55:43,172 DEBUG SimpleSubprocess cp "/tmp/tmpxdxfll9l/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_10kb.cool" 2021-09-03 15:55:43,280 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:55:43,297 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-03 15:55:43,297 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_20kb.cool 2021-09-03 15:55:43,297 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 15:55:43,298 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp_osx45hf/inter.cool" 2021-09-03 15:55:43,390 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 15:55:43,390 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp_osx45hf/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 15:55:46,509 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-03 15:55:46,510 DEBUG SimpleSubprocess cp "/tmp/tmp_osx45hf/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_20kb.cool" 2021-09-03 15:55:46,603 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:55:46,618 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-03 15:55:46,618 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_25kb.cool 2021-09-03 15:55:46,618 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 15:55:46,618 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpz1v1wg8k/inter.cool" 2021-09-03 15:55:46,703 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 15:55:46,703 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpz1v1wg8k/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 15:55:49,603 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-03 15:55:49,604 DEBUG SimpleSubprocess cp "/tmp/tmpz1v1wg8k/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_25kb.cool" 2021-09-03 15:55:49,696 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:55:49,708 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-03 15:55:49,708 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_50kb.cool 2021-09-03 15:55:49,708 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 15:55:49,709 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp4otmev35/inter.cool" 2021-09-03 15:55:49,783 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 15:55:49,783 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp4otmev35/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 15:55:52,156 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-03 15:55:52,156 DEBUG SimpleSubprocess cp "/tmp/tmp4otmev35/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_50kb.cool" 2021-09-03 15:55:52,226 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 15:55:52,238 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt 2021-09-03 15:55:52,247 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-03 15:55:52,248 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_5kb.cool 2021-09-03 15:55:52,248 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt 2021-09-03 15:55:52,248 INFO AddWeight Chromosome: chr2 2021-09-03 15:55:52,248 INFO AddWeight Resolution [bp]: 5000 2021-09-03 15:55:52,361 INFO AddWeight AddWeight successfully finished 2021-09-03 15:55:52,362 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_10kb.cool 2021-09-03 15:55:52,362 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt 2021-09-03 15:55:52,362 INFO AddWeight Chromosome: chr2 2021-09-03 15:55:52,362 INFO AddWeight Resolution [bp]: 10000 2021-09-03 15:55:52,407 INFO AddWeight AddWeight successfully finished 2021-09-03 15:55:52,407 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_20kb.cool 2021-09-03 15:55:52,407 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt 2021-09-03 15:55:52,407 INFO AddWeight Chromosome: chr2 2021-09-03 15:55:52,407 INFO AddWeight Resolution [bp]: 20000 2021-09-03 15:55:52,445 INFO AddWeight AddWeight successfully finished 2021-09-03 15:55:52,445 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_25kb.cool 2021-09-03 15:55:52,445 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt 2021-09-03 15:55:52,445 INFO AddWeight Chromosome: chr2 2021-09-03 15:55:52,445 INFO AddWeight Resolution [bp]: 25000 2021-09-03 15:55:52,478 INFO AddWeight AddWeight successfully finished 2021-09-03 15:55:52,478 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_50kb.cool 2021-09-03 15:55:52,478 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt 2021-09-03 15:55:52,478 INFO AddWeight Chromosome: chr2 2021-09-03 15:55:52,478 INFO AddWeight Resolution [bp]: 50000 2021-09-03 15:55:52,502 INFO AddWeight AddWeight successfully finished 2021-09-03 15:55:52,504 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.hic 2021-09-03 15:55:52,504 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_norm.hic 2021-09-03 15:55:52,504 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt 2021-09-03 15:55:52,504 INFO Vector2HiC Threads: 10 2021-09-03 15:55:52,532 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.hic" "/tmp/tmpx1hg3chf/inter.hic" 2021-09-03 15:55:53,375 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 15:55:53,375 INFO Vector2HiC Vector: vector c-tale_normalization chr2 5000 BP 2021-09-03 15:55:53,377 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpx1hg3chf/inter.hic" "/tmp/tmpx1hg3chf/vector.txt" 2021-09-03 15:55:58,730 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-03 15:55:58,730 INFO Vector2HiC Vector: vector c-tale_normalization chr2 10000 BP 2021-09-03 15:55:58,731 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpx1hg3chf/inter.hic" "/tmp/tmpx1hg3chf/vector.txt" 2021-09-03 15:56:03,225 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 15:56:03,225 INFO Vector2HiC Vector: vector c-tale_normalization chr2 20000 BP 2021-09-03 15:56:03,226 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpx1hg3chf/inter.hic" "/tmp/tmpx1hg3chf/vector.txt" 2021-09-03 15:56:07,080 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-03 15:56:07,080 INFO Vector2HiC Vector: vector c-tale_normalization chr2 25000 BP 2021-09-03 15:56:07,081 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpx1hg3chf/inter.hic" "/tmp/tmpx1hg3chf/vector.txt" 2021-09-03 15:56:11,245 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 15:56:11,246 INFO Vector2HiC Vector: vector c-tale_normalization chr2 50000 BP 2021-09-03 15:56:11,246 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpx1hg3chf/inter.hic" "/tmp/tmpx1hg3chf/vector.txt" 2021-09-03 15:56:15,423 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 15:56:15,424 DEBUG SimpleSubprocess cp "/tmp/tmpx1hg3chf/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_norm.hic" 2021-09-03 15:56:16,426 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-03 15:56:16,594 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/merged_nodups.txt" 2021-09-03 15:58:08,484 INFO SimpleSubprocess CopyResult - 0:01:51 2021-09-03 15:58:08,484 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter.pairs.txt" 2021-09-03 15:58:31,628 INFO SimpleSubprocess CopyResult - 0:00:23 2021-09-03 15:58:31,647 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/vector.txt" 2021-09-03 15:58:31,877 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 15:58:31,878 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter.hic" 2021-09-03 15:58:41,075 INFO SimpleSubprocess CopyResult - 0:00:09 2021-09-03 15:58:41,075 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_statistics.txt" 2021-09-03 15:58:41,148 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 15:58:41,148 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_no_balanced_5kb.cool" 2021-09-03 15:58:42,728 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 15:58:42,728 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_5kb.cool" 2021-09-03 15:58:44,393 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 15:58:44,393 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_no_balanced_10kb.cool" 2021-09-03 15:58:45,507 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 15:58:45,507 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_10kb.cool" 2021-09-03 15:58:46,739 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 15:58:46,739 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_no_balanced_20kb.cool" 2021-09-03 15:58:48,008 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 15:58:48,008 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_20kb.cool" 2021-09-03 15:58:49,166 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 15:58:49,167 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_no_balanced_25kb.cool" 2021-09-03 15:58:50,157 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 15:58:50,158 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_25kb.cool" 2021-09-03 15:58:50,839 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 15:58:50,840 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_no_balanced_50kb.cool" 2021-09-03 15:58:51,816 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 15:58:51,817 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/inter_50kb.cool" 2021-09-03 15:58:52,671 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 15:58:52,703 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855100-SRR5855101/__temp__" 2021-09-03 15:58:56,983 INFO SimpleSubprocess RemoveTemp - 0:00:04 2021-09-03 15:58:56,983 INFO BenchmarkPipeline 'SRR5855100-SRR5855101' FINISHED, SUMMARY TIME - 7:58:26