2021-09-28 02:46:45,262 INFO BenchmarkPipeline --- START PROCESSING 'SRR8453396-SRR8453397' --- 2021-09-28 02:46:45,262 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453396.sra 2021-09-28 02:46:45,262 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__ 2021-09-28 02:46:45,280 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpmtgybjc8 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453396.sra" 2021-09-28 02:57:45,909 INFO SimpleSubprocess Sra2FastQ - 0:11:00 2021-09-28 02:57:45,910 DEBUG SimpleSubprocess gzip /tmp/tmpmtgybjc8/* 2021-09-28 03:36:05,713 INFO SimpleSubprocess GZipFastQ - 0:38:19 2021-09-28 03:36:05,714 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/fastq"; mv /tmp/tmpmtgybjc8/SRR8453396_1.fastq.gz /tmp/tmpmtgybjc8/SRR8453396_R1.fastq.gz; mv /tmp/tmpmtgybjc8/SRR8453396_2.fastq.gz /tmp/tmpmtgybjc8/SRR8453396_R2.fastq.gz; cp /tmp/tmpmtgybjc8/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/fastq" 2021-09-28 03:36:10,210 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-28 03:36:11,208 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453397.sra 2021-09-28 03:36:11,209 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__ 2021-09-28 03:36:11,244 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpklfy9umo "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453397.sra" 2021-09-28 03:52:31,305 INFO SimpleSubprocess Sra2FastQ - 0:16:20 2021-09-28 03:52:31,331 DEBUG SimpleSubprocess gzip /tmp/tmpklfy9umo/* 2021-09-28 04:30:56,198 INFO SimpleSubprocess GZipFastQ - 0:38:24 2021-09-28 04:30:56,198 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/fastq"; mv /tmp/tmpklfy9umo/SRR8453397_2.fastq.gz /tmp/tmpklfy9umo/SRR8453397_R2.fastq.gz; mv /tmp/tmpklfy9umo/SRR8453397_1.fastq.gz /tmp/tmpklfy9umo/SRR8453397_R1.fastq.gz; cp /tmp/tmpklfy9umo/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/fastq" 2021-09-28 04:31:03,482 INFO SimpleSubprocess CopyFiles - 0:00:07 2021-09-28 04:31:04,548 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__ 2021-09-28 04:31:04,548 INFO Juicer Genome assembly: mm10 2021-09-28 04:31:04,548 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-28 04:31:04,548 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 04:31:04,548 INFO Juicer Enzyme: DpnII 2021-09-28 04:31:04,548 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-28 04:31:04,548 INFO Juicer Threads: 10 2021-09-28 04:31:04,548 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/HIC_tmp" 2021-09-28 04:31:04,583 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-28 04:31:04,584 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/SRR8453396-SRR8453397/__temp__" 2021-09-28 10:04:50,071 INFO SimpleSubprocess Juicer - 5:33:45 2021-09-28 10:04:50,156 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/SRR8453396-SRR8453397/__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/SRR8453396-SRR8453397/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453396_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453396_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453396.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453396.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453397_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453397_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453397.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/splits/SRR8453397.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 [2021-09-28T09:27:10,961] [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 [2021-09-28T09:49:04,622] [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/SRR8453396-SRR8453397/__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 [2021-09-28T10:04:49,337] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__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/SRR8453396-SRR8453397/__temp__/aligned for results 2021-09-28 10:04:50,358 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/merged_nodups.txt 2021-09-28 10:04:50,358 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt 2021-09-28 10:04:50,410 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpjg6mzn0n/inter.pairs.txt" 2021-09-28 10:05:33,736 INFO SimpleSubprocess MakeInterPairs - 0:00:43 2021-09-28 10:05:33,736 DEBUG SimpleSubprocess cp "/tmp/tmpjg6mzn0n/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt" 2021-09-28 10:05:34,908 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-28 10:05:35,156 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt 2021-09-28 10:05:35,156 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-28 10:05:35,156 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 10:05:35,156 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 10:05:35,156 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-28 10:05:35,156 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/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt" "/tmp/tmpqn1dsu5b/inter_no_balanced.cool" 2021-09-28 10:06:50,056 INFO SimpleSubprocess MakeCool - 0:01:14 2021-09-28 10:06:50,056 DEBUG SimpleSubprocess cp "/tmp/tmpqn1dsu5b/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-28 10:06:50,119 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:06:50,122 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt 2021-09-28 10:06:50,122 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-28 10:06:50,123 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 10:06:50,123 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 10:06:50,123 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-28 10:06:50,139 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/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt" "/tmp/tmpk146clvu/inter_no_balanced.cool" 2021-09-28 10:07:52,588 INFO SimpleSubprocess MakeCool - 0:01:02 2021-09-28 10:07:52,588 DEBUG SimpleSubprocess cp "/tmp/tmpk146clvu/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-28 10:07:52,611 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:07:52,635 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt 2021-09-28 10:07:52,635 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-28 10:07:52,635 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 10:07:52,635 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 10:07:52,635 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-28 10:07:52,636 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/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt" "/tmp/tmpgj_z78uo/inter_no_balanced.cool" 2021-09-28 10:08:50,938 INFO SimpleSubprocess MakeCool - 0:00:58 2021-09-28 10:08:50,938 DEBUG SimpleSubprocess cp "/tmp/tmpgj_z78uo/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-28 10:08:50,959 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:08:50,976 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt 2021-09-28 10:08:50,976 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-28 10:08:50,976 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 10:08:50,976 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 10:08:50,977 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-28 10:08:50,994 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/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt" "/tmp/tmp8ncjqvjw/inter_no_balanced.cool" 2021-09-28 10:09:48,711 INFO SimpleSubprocess MakeCool - 0:00:57 2021-09-28 10:09:48,711 DEBUG SimpleSubprocess cp "/tmp/tmp8ncjqvjw/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-28 10:09:48,730 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:09:48,753 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt 2021-09-28 10:09:48,753 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-28 10:09:48,753 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 10:09:48,753 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 10:09:48,753 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-28 10:09:48,754 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/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt" "/tmp/tmpumb3vl65/inter_no_balanced.cool" 2021-09-28 10:10:44,072 INFO SimpleSubprocess MakeCool - 0:00:55 2021-09-28 10:10:44,072 DEBUG SimpleSubprocess cp "/tmp/tmpumb3vl65/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-28 10:10:44,090 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:10:44,122 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-28 10:10:44,122 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_5kb.cool 2021-09-28 10:10:44,122 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 10:10:44,123 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmptjoapznb/inter.cool" 2021-09-28 10:10:44,151 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 10:10:44,151 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmptjoapznb/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 10:10:49,480 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-28 10:10:49,480 DEBUG SimpleSubprocess cp "/tmp/tmptjoapznb/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_5kb.cool" 2021-09-28 10:10:49,509 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:10:49,513 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-28 10:10:49,513 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_10kb.cool 2021-09-28 10:10:49,513 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 10:10:49,513 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp4qp9nqrb/inter.cool" 2021-09-28 10:10:49,537 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 10:10:49,537 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp4qp9nqrb/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 10:10:52,119 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-28 10:10:52,120 DEBUG SimpleSubprocess cp "/tmp/tmp4qp9nqrb/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_10kb.cool" 2021-09-28 10:10:52,144 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:10:52,147 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-28 10:10:52,147 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_20kb.cool 2021-09-28 10:10:52,147 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 10:10:52,166 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp9vpsqx7x/inter.cool" 2021-09-28 10:10:52,187 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 10:10:52,187 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp9vpsqx7x/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 10:10:54,124 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-28 10:10:54,124 DEBUG SimpleSubprocess cp "/tmp/tmp9vpsqx7x/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_20kb.cool" 2021-09-28 10:10:54,145 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:10:54,148 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-28 10:10:54,148 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_25kb.cool 2021-09-28 10:10:54,148 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 10:10:54,148 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmptamag4cy/inter.cool" 2021-09-28 10:10:54,168 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 10:10:54,169 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmptamag4cy/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 10:10:55,921 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-28 10:10:55,921 DEBUG SimpleSubprocess cp "/tmp/tmptamag4cy/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_25kb.cool" 2021-09-28 10:10:55,941 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:10:55,944 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-28 10:10:55,944 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_50kb.cool 2021-09-28 10:10:55,944 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 10:10:55,944 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp2balo7ty/inter.cool" 2021-09-28 10:10:55,962 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 10:10:55,962 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp2balo7ty/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 10:10:57,312 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-28 10:10:57,312 DEBUG SimpleSubprocess cp "/tmp/tmp2balo7ty/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_50kb.cool" 2021-09-28 10:10:57,330 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:10:57,334 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt 2021-09-28 10:10:57,340 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-28 10:10:57,359 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_5kb.cool 2021-09-28 10:10:57,359 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt 2021-09-28 10:10:57,359 INFO AddWeight Chromosome: chr11 2021-09-28 10:10:57,360 INFO AddWeight Resolution [bp]: 5000 2021-09-28 10:10:58,459 INFO AddWeight AddWeight successfully finished 2021-09-28 10:10:58,464 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_10kb.cool 2021-09-28 10:10:58,464 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt 2021-09-28 10:10:58,464 INFO AddWeight Chromosome: chr11 2021-09-28 10:10:58,465 INFO AddWeight Resolution [bp]: 10000 2021-09-28 10:10:58,518 INFO AddWeight AddWeight successfully finished 2021-09-28 10:10:58,518 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_20kb.cool 2021-09-28 10:10:58,518 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt 2021-09-28 10:10:58,518 INFO AddWeight Chromosome: chr11 2021-09-28 10:10:58,519 INFO AddWeight Resolution [bp]: 20000 2021-09-28 10:10:58,553 INFO AddWeight AddWeight successfully finished 2021-09-28 10:10:58,553 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_25kb.cool 2021-09-28 10:10:58,553 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt 2021-09-28 10:10:58,553 INFO AddWeight Chromosome: chr11 2021-09-28 10:10:58,553 INFO AddWeight Resolution [bp]: 25000 2021-09-28 10:10:58,584 INFO AddWeight AddWeight successfully finished 2021-09-28 10:10:58,584 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_50kb.cool 2021-09-28 10:10:58,584 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt 2021-09-28 10:10:58,584 INFO AddWeight Chromosome: chr11 2021-09-28 10:10:58,584 INFO AddWeight Resolution [bp]: 50000 2021-09-28 10:10:58,608 INFO AddWeight AddWeight successfully finished 2021-09-28 10:10:58,610 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.hic 2021-09-28 10:10:58,610 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_norm.hic 2021-09-28 10:10:58,610 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt 2021-09-28 10:10:58,610 INFO Vector2HiC Threads: 10 2021-09-28 10:10:58,632 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.hic" "/tmp/tmp4sh1pk4f/inter.hic" 2021-09-28 10:10:58,897 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 10:10:58,897 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-09-28 10:10:58,899 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp4sh1pk4f/inter.hic" "/tmp/tmp4sh1pk4f/vector.txt" 2021-09-28 10:11:03,779 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 10:11:03,780 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-09-28 10:11:03,781 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp4sh1pk4f/inter.hic" "/tmp/tmp4sh1pk4f/vector.txt" 2021-09-28 10:11:08,073 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 10:11:08,073 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-09-28 10:11:08,074 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp4sh1pk4f/inter.hic" "/tmp/tmp4sh1pk4f/vector.txt" 2021-09-28 10:11:12,066 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-28 10:11:12,067 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-09-28 10:11:12,067 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp4sh1pk4f/inter.hic" "/tmp/tmp4sh1pk4f/vector.txt" 2021-09-28 10:11:16,163 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 10:11:16,164 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-09-28 10:11:16,164 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp4sh1pk4f/inter.hic" "/tmp/tmp4sh1pk4f/vector.txt" 2021-09-28 10:11:20,282 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 10:11:20,282 DEBUG SimpleSubprocess cp "/tmp/tmp4sh1pk4f/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_norm.hic" 2021-09-28 10:11:20,633 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 10:11:20,728 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/merged_nodups.txt" 2021-09-28 10:11:40,479 INFO SimpleSubprocess CopyResult - 0:00:19 2021-09-28 10:11:40,479 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter.pairs.txt" 2021-09-28 10:11:50,128 INFO SimpleSubprocess CopyResult - 0:00:09 2021-09-28 10:11:50,128 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/vector.txt" 2021-09-28 10:11:50,136 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:50,136 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter.hic" 2021-09-28 10:11:52,740 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-28 10:11:52,740 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_statistics.txt" 2021-09-28 10:11:52,747 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:52,747 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_no_balanced_5kb.cool" 2021-09-28 10:11:52,867 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:52,867 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_5kb.cool" 2021-09-28 10:11:52,973 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:52,973 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_no_balanced_10kb.cool" 2021-09-28 10:11:53,096 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:53,096 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_10kb.cool" 2021-09-28 10:11:53,228 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:53,229 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_no_balanced_20kb.cool" 2021-09-28 10:11:53,330 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:53,331 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_20kb.cool" 2021-09-28 10:11:53,435 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:53,435 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_no_balanced_25kb.cool" 2021-09-28 10:11:53,552 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:53,552 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_25kb.cool" 2021-09-28 10:11:53,620 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:53,620 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_no_balanced_50kb.cool" 2021-09-28 10:11:53,692 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:53,692 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/inter_50kb.cool" 2021-09-28 10:11:53,775 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 10:11:54,017 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453396-SRR8453397/__temp__" 2021-09-28 10:12:05,467 INFO SimpleSubprocess RemoveTemp - 0:00:11 2021-09-28 10:12:05,467 INFO BenchmarkPipeline 'SRR8453396-SRR8453397' FINISHED, SUMMARY TIME - 7:25:20