2021-09-30 10:05:47,262 INFO BenchmarkPipeline --- START PROCESSING 'SRR8984913-SRR8984914' --- 2021-09-30 10:05:47,262 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984913.sra 2021-09-30 10:05:47,262 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__ 2021-09-30 10:05:47,263 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp0uzqcjeq "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984913.sra" 2021-09-30 10:23:36,860 INFO SimpleSubprocess Sra2FastQ - 0:17:49 2021-09-30 10:23:36,875 DEBUG SimpleSubprocess gzip /tmp/tmp0uzqcjeq/* 2021-09-30 11:17:43,495 INFO SimpleSubprocess GZipFastQ - 0:54:06 2021-09-30 11:17:43,525 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/fastq"; mv /tmp/tmp0uzqcjeq/SRR8984913_2.fastq.gz /tmp/tmp0uzqcjeq/SRR8984913_R2.fastq.gz; mv /tmp/tmp0uzqcjeq/SRR8984913_1.fastq.gz /tmp/tmp0uzqcjeq/SRR8984913_R1.fastq.gz; cp /tmp/tmp0uzqcjeq/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/fastq" 2021-09-30 11:18:03,260 INFO SimpleSubprocess CopyFiles - 0:00:19 2021-09-30 11:18:04,508 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984914.sra 2021-09-30 11:18:04,508 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__ 2021-09-30 11:18:04,541 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpy1g77fjm "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984914.sra" 2021-09-30 11:34:53,903 INFO SimpleSubprocess Sra2FastQ - 0:16:49 2021-09-30 11:34:53,917 DEBUG SimpleSubprocess gzip /tmp/tmpy1g77fjm/* 2021-09-30 12:26:11,809 INFO SimpleSubprocess GZipFastQ - 0:51:17 2021-09-30 12:26:11,810 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/fastq"; mv /tmp/tmpy1g77fjm/SRR8984914_2.fastq.gz /tmp/tmpy1g77fjm/SRR8984914_R2.fastq.gz; mv /tmp/tmpy1g77fjm/SRR8984914_1.fastq.gz /tmp/tmpy1g77fjm/SRR8984914_R1.fastq.gz; cp /tmp/tmpy1g77fjm/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/fastq" 2021-09-30 12:26:26,564 INFO SimpleSubprocess CopyFiles - 0:00:14 2021-09-30 12:26:28,156 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__ 2021-09-30 12:26:28,156 INFO Juicer Genome assembly: mm10 2021-09-30 12:26:28,156 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-30 12:26:28,156 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 12:26:28,156 INFO Juicer Enzyme: DpnII 2021-09-30 12:26:28,156 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-30 12:26:28,156 INFO Juicer Threads: 10 2021-09-30 12:26:28,157 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/HIC_tmp" 2021-09-30 12:26:28,204 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-30 12:26:28,204 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/SRR8984913-SRR8984914/__temp__" 2021-09-30 23:13:45,049 INFO SimpleSubprocess Juicer - 10:47:16 2021-09-30 23:13:45,117 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/SRR8984913-SRR8984914/__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/SRR8984913-SRR8984914/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984913_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984913_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984913.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984913.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984914_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984914_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984914.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/splits/SRR8984914.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 [2021-09-30T21:42:17,688] [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 [2021-09-30T22:35:51,308] [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/SRR8984913-SRR8984914/__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 [2021-09-30T23:13:44,402] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__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/SRR8984913-SRR8984914/__temp__/aligned for results 2021-09-30 23:13:45,222 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/merged_nodups.txt 2021-09-30 23:13:45,224 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt 2021-09-30 23:13:45,344 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpr8io16rx/inter.pairs.txt" 2021-09-30 23:15:39,333 INFO SimpleSubprocess MakeInterPairs - 0:01:53 2021-09-30 23:15:39,333 DEBUG SimpleSubprocess cp "/tmp/tmpr8io16rx/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt" 2021-09-30 23:15:42,052 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-30 23:15:42,486 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt 2021-09-30 23:15:42,487 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-30 23:15:42,487 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 23:15:42,487 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 23:15:42,487 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-30 23:15:42,530 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/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2e0rtkjw/inter_no_balanced.cool" 2021-09-30 23:18:30,998 INFO SimpleSubprocess MakeCool - 0:02:48 2021-09-30 23:18:30,998 DEBUG SimpleSubprocess cp "/tmp/tmp2e0rtkjw/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-30 23:18:31,061 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:18:31,069 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt 2021-09-30 23:18:31,069 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-30 23:18:31,069 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 23:18:31,069 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 23:18:31,069 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-30 23:18:31,102 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/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt" "/tmp/tmp5bmkp9je/inter_no_balanced.cool" 2021-09-30 23:21:04,837 INFO SimpleSubprocess MakeCool - 0:02:33 2021-09-30 23:21:04,837 DEBUG SimpleSubprocess cp "/tmp/tmp5bmkp9je/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-30 23:21:04,887 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:21:04,894 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt 2021-09-30 23:21:04,894 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-30 23:21:04,894 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 23:21:04,894 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 23:21:04,895 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-30 23:21:04,917 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/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt" "/tmp/tmp18wtog2l/inter_no_balanced.cool" 2021-09-30 23:23:30,294 INFO SimpleSubprocess MakeCool - 0:02:25 2021-09-30 23:23:30,294 DEBUG SimpleSubprocess cp "/tmp/tmp18wtog2l/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-30 23:23:30,342 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:23:30,603 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt 2021-09-30 23:23:30,603 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-30 23:23:30,603 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 23:23:30,603 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 23:23:30,603 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-30 23:23:30,603 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/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt" "/tmp/tmp_qs100cr/inter_no_balanced.cool" 2021-09-30 23:25:54,739 INFO SimpleSubprocess MakeCool - 0:02:24 2021-09-30 23:25:54,739 DEBUG SimpleSubprocess cp "/tmp/tmp_qs100cr/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-30 23:25:54,780 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:25:54,786 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt 2021-09-30 23:25:54,786 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-30 23:25:54,786 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 23:25:54,786 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 23:25:54,786 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-30 23:25:54,787 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/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt" "/tmp/tmp887zxany/inter_no_balanced.cool" 2021-09-30 23:28:12,635 INFO SimpleSubprocess MakeCool - 0:02:17 2021-09-30 23:28:12,635 DEBUG SimpleSubprocess cp "/tmp/tmp887zxany/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-30 23:28:12,673 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:28:12,708 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-30 23:28:12,708 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_5kb.cool 2021-09-30 23:28:12,708 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 23:28:12,715 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp2cm1yesp/inter.cool" 2021-09-30 23:28:12,778 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 23:28:12,778 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp2cm1yesp/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 23:28:29,317 INFO SimpleSubprocess NormalizeCool - 0:00:16 2021-09-30 23:28:29,317 DEBUG SimpleSubprocess cp "/tmp/tmp2cm1yesp/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_5kb.cool" 2021-09-30 23:28:29,375 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:28:29,383 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-30 23:28:29,383 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_10kb.cool 2021-09-30 23:28:29,383 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 23:28:29,412 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpoqh7po4b/inter.cool" 2021-09-30 23:28:29,461 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 23:28:29,462 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpoqh7po4b/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 23:28:41,227 INFO SimpleSubprocess NormalizeCool - 0:00:11 2021-09-30 23:28:41,228 DEBUG SimpleSubprocess cp "/tmp/tmpoqh7po4b/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_10kb.cool" 2021-09-30 23:28:41,277 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:28:41,308 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-30 23:28:41,308 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_20kb.cool 2021-09-30 23:28:41,308 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 23:28:41,314 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpby209bpz/inter.cool" 2021-09-30 23:28:41,358 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 23:28:41,358 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpby209bpz/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 23:28:49,087 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-30 23:28:49,087 DEBUG SimpleSubprocess cp "/tmp/tmpby209bpz/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_20kb.cool" 2021-09-30 23:28:49,131 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:28:49,137 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-30 23:28:49,137 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_25kb.cool 2021-09-30 23:28:49,137 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 23:28:49,159 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp85ksdsqy/inter.cool" 2021-09-30 23:28:49,200 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 23:28:49,200 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp85ksdsqy/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 23:28:56,554 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-30 23:28:56,555 DEBUG SimpleSubprocess cp "/tmp/tmp85ksdsqy/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_25kb.cool" 2021-09-30 23:28:56,595 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:28:56,601 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-30 23:28:56,601 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_50kb.cool 2021-09-30 23:28:56,601 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 23:28:56,601 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp3t65frjj/inter.cool" 2021-09-30 23:28:56,636 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 23:28:56,636 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3t65frjj/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 23:29:01,153 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-30 23:29:01,153 DEBUG SimpleSubprocess cp "/tmp/tmp3t65frjj/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_50kb.cool" 2021-09-30 23:29:01,188 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:29:01,194 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt 2021-09-30 23:29:01,201 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-30 23:29:01,201 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_5kb.cool 2021-09-30 23:29:01,201 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt 2021-09-30 23:29:01,201 INFO AddWeight Chromosome: chr5 2021-09-30 23:29:01,201 INFO AddWeight Resolution [bp]: 5000 2021-09-30 23:29:02,146 INFO AddWeight AddWeight successfully finished 2021-09-30 23:29:02,146 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_10kb.cool 2021-09-30 23:29:02,146 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt 2021-09-30 23:29:02,146 INFO AddWeight Chromosome: chr5 2021-09-30 23:29:02,146 INFO AddWeight Resolution [bp]: 10000 2021-09-30 23:29:02,194 INFO AddWeight AddWeight successfully finished 2021-09-30 23:29:02,194 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_20kb.cool 2021-09-30 23:29:02,194 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt 2021-09-30 23:29:02,194 INFO AddWeight Chromosome: chr5 2021-09-30 23:29:02,195 INFO AddWeight Resolution [bp]: 20000 2021-09-30 23:29:02,221 INFO AddWeight AddWeight successfully finished 2021-09-30 23:29:02,221 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_25kb.cool 2021-09-30 23:29:02,221 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt 2021-09-30 23:29:02,221 INFO AddWeight Chromosome: chr5 2021-09-30 23:29:02,221 INFO AddWeight Resolution [bp]: 25000 2021-09-30 23:29:02,244 INFO AddWeight AddWeight successfully finished 2021-09-30 23:29:02,245 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_50kb.cool 2021-09-30 23:29:02,245 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt 2021-09-30 23:29:02,245 INFO AddWeight Chromosome: chr5 2021-09-30 23:29:02,245 INFO AddWeight Resolution [bp]: 50000 2021-09-30 23:29:02,263 INFO AddWeight AddWeight successfully finished 2021-09-30 23:29:02,265 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.hic 2021-09-30 23:29:02,265 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_norm.hic 2021-09-30 23:29:02,265 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt 2021-09-30 23:29:02,265 INFO Vector2HiC Threads: 10 2021-09-30 23:29:02,333 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.hic" "/tmp/tmphsfsbrb1/inter.hic" 2021-09-30 23:29:02,743 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 23:29:02,743 INFO Vector2HiC Vector: vector c-tale_normalization chr5 5000 BP 2021-09-30 23:29:02,744 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmphsfsbrb1/inter.hic" "/tmp/tmphsfsbrb1/vector.txt" 2021-09-30 23:29:07,207 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 23:29:07,207 INFO Vector2HiC Vector: vector c-tale_normalization chr5 10000 BP 2021-09-30 23:29:07,209 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmphsfsbrb1/inter.hic" "/tmp/tmphsfsbrb1/vector.txt" 2021-09-30 23:29:11,376 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 23:29:11,376 INFO Vector2HiC Vector: vector c-tale_normalization chr5 20000 BP 2021-09-30 23:29:11,376 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmphsfsbrb1/inter.hic" "/tmp/tmphsfsbrb1/vector.txt" 2021-09-30 23:29:15,214 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-30 23:29:15,215 INFO Vector2HiC Vector: vector c-tale_normalization chr5 25000 BP 2021-09-30 23:29:15,215 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmphsfsbrb1/inter.hic" "/tmp/tmphsfsbrb1/vector.txt" 2021-09-30 23:29:19,386 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 23:29:19,386 INFO Vector2HiC Vector: vector c-tale_normalization chr5 50000 BP 2021-09-30 23:29:19,387 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmphsfsbrb1/inter.hic" "/tmp/tmphsfsbrb1/vector.txt" 2021-09-30 23:29:23,534 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 23:29:23,534 DEBUG SimpleSubprocess cp "/tmp/tmphsfsbrb1/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_norm.hic" 2021-09-30 23:29:24,026 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 23:29:24,112 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/merged_nodups.txt" 2021-09-30 23:31:42,242 INFO SimpleSubprocess CopyResult - 0:02:18 2021-09-30 23:31:42,257 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter.pairs.txt" 2021-09-30 23:32:02,717 INFO SimpleSubprocess CopyResult - 0:00:20 2021-09-30 23:32:02,718 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/vector.txt" 2021-09-30 23:32:02,756 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:02,756 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter.hic" 2021-09-30 23:32:07,962 INFO SimpleSubprocess CopyResult - 0:00:05 2021-09-30 23:32:07,962 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_statistics.txt" 2021-09-30 23:32:07,970 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:07,970 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_no_balanced_5kb.cool" 2021-09-30 23:32:08,802 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:08,802 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_5kb.cool" 2021-09-30 23:32:09,406 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:09,406 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_no_balanced_10kb.cool" 2021-09-30 23:32:10,069 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:10,069 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_10kb.cool" 2021-09-30 23:32:11,034 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:11,034 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_no_balanced_20kb.cool" 2021-09-30 23:32:11,387 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:11,387 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_20kb.cool" 2021-09-30 23:32:11,709 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:11,709 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_no_balanced_25kb.cool" 2021-09-30 23:32:12,235 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:12,236 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_25kb.cool" 2021-09-30 23:32:12,508 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:12,508 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_no_balanced_50kb.cool" 2021-09-30 23:32:13,142 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:13,142 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/inter_50kb.cool" 2021-09-30 23:32:13,341 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 23:32:13,390 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984913-SRR8984914/__temp__" 2021-09-30 23:32:30,915 INFO SimpleSubprocess RemoveTemp - 0:00:17 2021-09-30 23:32:30,915 INFO BenchmarkPipeline 'SRR8984913-SRR8984914' FINISHED, SUMMARY TIME - 13:26:43