2021-09-28 10:12:05,677 INFO BenchmarkPipeline --- START PROCESSING 'SRR8453398-SRR8453399' --- 2021-09-28 10:12:05,677 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453398.sra 2021-09-28 10:12:05,677 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__ 2021-09-28 10:12:05,677 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpdlnt9nsp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453398.sra" 2021-09-28 10:32:09,568 INFO SimpleSubprocess Sra2FastQ - 0:20:03 2021-09-28 10:32:09,587 DEBUG SimpleSubprocess gzip /tmp/tmpdlnt9nsp/* 2021-09-28 11:21:24,827 INFO SimpleSubprocess GZipFastQ - 0:49:15 2021-09-28 11:21:24,939 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/fastq"; mv /tmp/tmpdlnt9nsp/SRR8453398_1.fastq.gz /tmp/tmpdlnt9nsp/SRR8453398_R1.fastq.gz; mv /tmp/tmpdlnt9nsp/SRR8453398_2.fastq.gz /tmp/tmpdlnt9nsp/SRR8453398_R2.fastq.gz; cp /tmp/tmpdlnt9nsp/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/fastq" 2021-09-28 11:21:48,352 INFO SimpleSubprocess CopyFiles - 0:00:23 2021-09-28 11:21:49,694 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453399.sra 2021-09-28 11:21:49,694 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__ 2021-09-28 11:21:49,695 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpoarx0hug "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453399.sra" 2021-09-28 11:35:12,358 INFO SimpleSubprocess Sra2FastQ - 0:13:22 2021-09-28 11:35:12,381 DEBUG SimpleSubprocess gzip /tmp/tmpoarx0hug/* 2021-09-28 12:06:20,601 INFO SimpleSubprocess GZipFastQ - 0:31:08 2021-09-28 12:06:20,602 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/fastq"; mv /tmp/tmpoarx0hug/SRR8453399_2.fastq.gz /tmp/tmpoarx0hug/SRR8453399_R2.fastq.gz; mv /tmp/tmpoarx0hug/SRR8453399_1.fastq.gz /tmp/tmpoarx0hug/SRR8453399_R1.fastq.gz; cp /tmp/tmpoarx0hug/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/fastq" 2021-09-28 12:06:26,303 INFO SimpleSubprocess CopyFiles - 0:00:05 2021-09-28 12:06:27,233 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__ 2021-09-28 12:06:27,233 INFO Juicer Genome assembly: mm10 2021-09-28 12:06:27,234 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-28 12:06:27,234 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 12:06:27,234 INFO Juicer Enzyme: DpnII 2021-09-28 12:06:27,234 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-28 12:06:27,234 INFO Juicer Threads: 10 2021-09-28 12:06:27,234 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/HIC_tmp" 2021-09-28 12:06:27,275 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-28 12:06:27,275 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/SRR8453398-SRR8453399/__temp__" 2021-09-28 20:30:42,444 INFO SimpleSubprocess Juicer - 8:24:15 2021-09-28 20:30:42,586 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/SRR8453398-SRR8453399/__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/SRR8453398-SRR8453399/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453398_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453398_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453398.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453398.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453399_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453399_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453399.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/splits/SRR8453399.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 [2021-09-28T19:22:35,954] [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 [2021-09-28T20:01:32,899] [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/SRR8453398-SRR8453399/__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 [2021-09-28T20:30:41,433] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__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/SRR8453398-SRR8453399/__temp__/aligned for results 2021-09-28 20:30:42,836 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/merged_nodups.txt 2021-09-28 20:30:42,836 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt 2021-09-28 20:30:42,962 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp1s3a0d9p/inter.pairs.txt" 2021-09-28 20:31:42,580 INFO SimpleSubprocess MakeInterPairs - 0:00:59 2021-09-28 20:31:42,580 DEBUG SimpleSubprocess cp "/tmp/tmp1s3a0d9p/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt" 2021-09-28 20:31:44,233 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-28 20:31:45,463 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt 2021-09-28 20:31:45,463 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-28 20:31:45,463 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 20:31:45,463 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 20:31:45,488 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-28 20:31:45,488 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/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt" "/tmp/tmp340w3cgn/inter_no_balanced.cool" 2021-09-28 20:33:26,923 INFO SimpleSubprocess MakeCool - 0:01:41 2021-09-28 20:33:26,923 DEBUG SimpleSubprocess cp "/tmp/tmp340w3cgn/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-28 20:33:26,958 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:33:26,991 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt 2021-09-28 20:33:27,004 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-28 20:33:27,004 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 20:33:27,004 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 20:33:27,005 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-28 20:33:27,036 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/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2u6zgm_s/inter_no_balanced.cool" 2021-09-28 20:34:53,564 INFO SimpleSubprocess MakeCool - 0:01:26 2021-09-28 20:34:53,564 DEBUG SimpleSubprocess cp "/tmp/tmp2u6zgm_s/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-28 20:34:53,594 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:34:53,598 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt 2021-09-28 20:34:53,598 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-28 20:34:53,599 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 20:34:53,599 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 20:34:53,599 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-28 20:34:53,599 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/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt" "/tmp/tmp814wlaz1/inter_no_balanced.cool" 2021-09-28 20:36:17,127 INFO SimpleSubprocess MakeCool - 0:01:23 2021-09-28 20:36:17,127 DEBUG SimpleSubprocess cp "/tmp/tmp814wlaz1/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-28 20:36:17,156 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:36:17,159 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt 2021-09-28 20:36:17,159 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-28 20:36:17,159 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 20:36:17,159 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 20:36:17,159 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-28 20:36:17,186 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/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt" "/tmp/tmpihsisy4o/inter_no_balanced.cool" 2021-09-28 20:37:39,665 INFO SimpleSubprocess MakeCool - 0:01:22 2021-09-28 20:37:39,666 DEBUG SimpleSubprocess cp "/tmp/tmpihsisy4o/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-28 20:37:39,692 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:37:39,711 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt 2021-09-28 20:37:39,711 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-28 20:37:39,711 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 20:37:39,711 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 20:37:39,711 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-28 20:37:39,711 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/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt" "/tmp/tmpe8jsrbif/inter_no_balanced.cool" 2021-09-28 20:38:57,569 INFO SimpleSubprocess MakeCool - 0:01:17 2021-09-28 20:38:57,570 DEBUG SimpleSubprocess cp "/tmp/tmpe8jsrbif/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-28 20:38:57,591 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:38:57,657 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-28 20:38:57,658 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_5kb.cool 2021-09-28 20:38:57,658 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 20:38:57,658 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmprrwbje4v/inter.cool" 2021-09-28 20:38:57,692 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 20:38:57,693 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmprrwbje4v/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 20:39:03,131 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-28 20:39:03,132 DEBUG SimpleSubprocess cp "/tmp/tmprrwbje4v/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_5kb.cool" 2021-09-28 20:39:03,189 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:39:03,194 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-28 20:39:03,194 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_10kb.cool 2021-09-28 20:39:03,194 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 20:39:03,223 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpb51d87k2/inter.cool" 2021-09-28 20:39:03,253 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 20:39:03,253 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpb51d87k2/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 20:39:05,987 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-28 20:39:05,987 DEBUG SimpleSubprocess cp "/tmp/tmpb51d87k2/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_10kb.cool" 2021-09-28 20:39:06,017 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:39:06,021 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-28 20:39:06,021 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_20kb.cool 2021-09-28 20:39:06,021 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 20:39:06,021 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpdsazj8fy/inter.cool" 2021-09-28 20:39:06,047 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 20:39:06,047 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpdsazj8fy/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 20:39:08,038 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-28 20:39:08,038 DEBUG SimpleSubprocess cp "/tmp/tmpdsazj8fy/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_20kb.cool" 2021-09-28 20:39:08,067 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:39:08,070 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-28 20:39:08,070 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_25kb.cool 2021-09-28 20:39:08,070 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 20:39:08,096 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp5y4skf27/inter.cool" 2021-09-28 20:39:08,123 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 20:39:08,123 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp5y4skf27/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 20:39:09,874 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-28 20:39:09,874 DEBUG SimpleSubprocess cp "/tmp/tmp5y4skf27/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_25kb.cool" 2021-09-28 20:39:09,899 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:39:09,940 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-28 20:39:09,940 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_50kb.cool 2021-09-28 20:39:09,940 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-28 20:39:09,940 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpy4fud_r9/inter.cool" 2021-09-28 20:39:09,961 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 20:39:09,961 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpy4fud_r9/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-28 20:39:11,223 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-28 20:39:11,223 DEBUG SimpleSubprocess cp "/tmp/tmpy4fud_r9/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_50kb.cool" 2021-09-28 20:39:11,244 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:39:11,260 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt 2021-09-28 20:39:11,266 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-28 20:39:11,309 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_5kb.cool 2021-09-28 20:39:11,309 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt 2021-09-28 20:39:11,309 INFO AddWeight Chromosome: chr11 2021-09-28 20:39:11,309 INFO AddWeight Resolution [bp]: 5000 2021-09-28 20:39:13,159 INFO AddWeight AddWeight successfully finished 2021-09-28 20:39:13,160 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_10kb.cool 2021-09-28 20:39:13,160 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt 2021-09-28 20:39:13,160 INFO AddWeight Chromosome: chr11 2021-09-28 20:39:13,160 INFO AddWeight Resolution [bp]: 10000 2021-09-28 20:39:13,209 INFO AddWeight AddWeight successfully finished 2021-09-28 20:39:13,209 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_20kb.cool 2021-09-28 20:39:13,209 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt 2021-09-28 20:39:13,209 INFO AddWeight Chromosome: chr11 2021-09-28 20:39:13,209 INFO AddWeight Resolution [bp]: 20000 2021-09-28 20:39:13,240 INFO AddWeight AddWeight successfully finished 2021-09-28 20:39:13,240 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_25kb.cool 2021-09-28 20:39:13,240 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt 2021-09-28 20:39:13,240 INFO AddWeight Chromosome: chr11 2021-09-28 20:39:13,240 INFO AddWeight Resolution [bp]: 25000 2021-09-28 20:39:13,267 INFO AddWeight AddWeight successfully finished 2021-09-28 20:39:13,267 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_50kb.cool 2021-09-28 20:39:13,267 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt 2021-09-28 20:39:13,267 INFO AddWeight Chromosome: chr11 2021-09-28 20:39:13,268 INFO AddWeight Resolution [bp]: 50000 2021-09-28 20:39:13,288 INFO AddWeight AddWeight successfully finished 2021-09-28 20:39:13,315 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.hic 2021-09-28 20:39:13,315 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_norm.hic 2021-09-28 20:39:13,315 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt 2021-09-28 20:39:13,315 INFO Vector2HiC Threads: 10 2021-09-28 20:39:13,363 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.hic" "/tmp/tmpw87g22q_/inter.hic" 2021-09-28 20:39:13,649 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 20:39:13,649 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-09-28 20:39:13,651 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpw87g22q_/inter.hic" "/tmp/tmpw87g22q_/vector.txt" 2021-09-28 20:39:18,251 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 20:39:18,251 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-09-28 20:39:18,252 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpw87g22q_/inter.hic" "/tmp/tmpw87g22q_/vector.txt" 2021-09-28 20:39:22,094 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-28 20:39:22,094 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-09-28 20:39:22,095 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpw87g22q_/inter.hic" "/tmp/tmpw87g22q_/vector.txt" 2021-09-28 20:39:25,787 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-28 20:39:25,787 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-09-28 20:39:25,789 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpw87g22q_/inter.hic" "/tmp/tmpw87g22q_/vector.txt" 2021-09-28 20:39:29,584 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-28 20:39:29,584 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-09-28 20:39:29,585 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpw87g22q_/inter.hic" "/tmp/tmpw87g22q_/vector.txt" 2021-09-28 20:39:33,605 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 20:39:33,605 DEBUG SimpleSubprocess cp "/tmp/tmpw87g22q_/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_norm.hic" 2021-09-28 20:39:33,962 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 20:39:34,092 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/merged_nodups.txt" 2021-09-28 20:40:05,444 INFO SimpleSubprocess CopyResult - 0:00:31 2021-09-28 20:40:05,444 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter.pairs.txt" 2021-09-28 20:40:18,755 INFO SimpleSubprocess CopyResult - 0:00:13 2021-09-28 20:40:18,755 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/vector.txt" 2021-09-28 20:40:18,764 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:18,764 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter.hic" 2021-09-28 20:40:21,663 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-28 20:40:21,663 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_statistics.txt" 2021-09-28 20:40:21,671 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:21,671 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_no_balanced_5kb.cool" 2021-09-28 20:40:21,916 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:21,916 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_5kb.cool" 2021-09-28 20:40:22,148 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:22,148 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_no_balanced_10kb.cool" 2021-09-28 20:40:22,359 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:22,359 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_10kb.cool" 2021-09-28 20:40:22,571 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:22,571 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_no_balanced_20kb.cool" 2021-09-28 20:40:22,732 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:22,732 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_20kb.cool" 2021-09-28 20:40:22,911 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:22,911 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_no_balanced_25kb.cool" 2021-09-28 20:40:23,047 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:23,047 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_25kb.cool" 2021-09-28 20:40:23,171 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:23,172 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_no_balanced_50kb.cool" 2021-09-28 20:40:23,283 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:23,283 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/inter_50kb.cool" 2021-09-28 20:40:23,375 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 20:40:23,605 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453398-SRR8453399/__temp__" 2021-09-28 20:40:37,674 INFO SimpleSubprocess RemoveTemp - 0:00:14 2021-09-28 20:40:37,675 INFO BenchmarkPipeline 'SRR8453398-SRR8453399' FINISHED, SUMMARY TIME - 10:28:31