2021-09-22 23:56:03,351 INFO BenchmarkPipeline --- START PROCESSING 'SRR7500318' --- 2021-09-22 23:56:03,352 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500318.sra 2021-09-22 23:56:03,352 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__ 2021-09-22 23:56:03,352 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmplr9omrds "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500318.sra" 2021-09-23 00:16:25,078 INFO SimpleSubprocess Sra2FastQ - 0:20:21 2021-09-23 00:16:25,099 DEBUG SimpleSubprocess gzip /tmp/tmplr9omrds/* 2021-09-23 01:10:56,135 INFO SimpleSubprocess GZipFastQ - 0:54:31 2021-09-23 01:10:56,135 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/fastq"; mv /tmp/tmplr9omrds/SRR7500318_1.fastq.gz /tmp/tmplr9omrds/SRR7500318_R1.fastq.gz; mv /tmp/tmplr9omrds/SRR7500318_2.fastq.gz /tmp/tmplr9omrds/SRR7500318_R2.fastq.gz; cp /tmp/tmplr9omrds/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/fastq" 2021-09-23 01:11:29,357 INFO SimpleSubprocess CopyFiles - 0:00:33 2021-09-23 01:11:30,995 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__ 2021-09-23 01:11:30,995 INFO Juicer Genome assembly: mm10 2021-09-23 01:11:30,995 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-23 01:11:30,995 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 01:11:30,995 INFO Juicer Enzyme: DpnII 2021-09-23 01:11:30,995 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-23 01:11:30,995 INFO Juicer Threads: 10 2021-09-23 01:11:30,995 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/HIC_tmp" 2021-09-23 01:11:31,048 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-23 01:11:31,049 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/SRR7500318/__temp__" 2021-09-23 06:54:57,374 INFO SimpleSubprocess Juicer - 5:43:26 2021-09-23 06:54:57,406 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/SRR7500318/__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/SRR7500318/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/splits/SRR7500318_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/splits/SRR7500318_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/splits/SRR7500318.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/splits/SRR7500318.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 [2021-09-23T05:23:53,400] [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 [2021-09-23T06:37:44,465] [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/SRR7500318/__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 [2021-09-23T06:54:57,042] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__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/SRR7500318/__temp__/aligned for results 2021-09-23 06:54:57,471 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/merged_nodups.txt 2021-09-23 06:54:57,471 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt 2021-09-23 06:54:57,491 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpqk5v8z25/inter.pairs.txt" 2021-09-23 06:55:43,237 INFO SimpleSubprocess MakeInterPairs - 0:00:45 2021-09-23 06:55:43,237 DEBUG SimpleSubprocess cp "/tmp/tmpqk5v8z25/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt" 2021-09-23 06:55:44,479 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-23 06:55:45,257 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt 2021-09-23 06:55:45,257 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-23 06:55:45,258 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 06:55:45,258 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 06:55:45,258 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-23 06:55:45,258 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/SRR7500318/__temp__/aligned/inter.pairs.txt" "/tmp/tmpietgqnxb/inter_no_balanced.cool" 2021-09-23 06:56:59,583 INFO SimpleSubprocess MakeCool - 0:01:14 2021-09-23 06:56:59,583 DEBUG SimpleSubprocess cp "/tmp/tmpietgqnxb/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-23 06:56:59,646 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 06:56:59,649 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt 2021-09-23 06:56:59,649 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-23 06:56:59,649 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 06:56:59,650 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 06:56:59,650 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-23 06:56:59,650 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/SRR7500318/__temp__/aligned/inter.pairs.txt" "/tmp/tmpzpxjr3g6/inter_no_balanced.cool" 2021-09-23 06:58:04,761 INFO SimpleSubprocess MakeCool - 0:01:05 2021-09-23 06:58:04,762 DEBUG SimpleSubprocess cp "/tmp/tmpzpxjr3g6/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-23 06:58:04,785 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 06:58:04,788 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt 2021-09-23 06:58:04,788 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-23 06:58:04,788 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 06:58:04,788 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 06:58:04,788 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-23 06:58:04,789 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/SRR7500318/__temp__/aligned/inter.pairs.txt" "/tmp/tmp035k5jyg/inter_no_balanced.cool" 2021-09-23 06:59:06,983 INFO SimpleSubprocess MakeCool - 0:01:02 2021-09-23 06:59:06,984 DEBUG SimpleSubprocess cp "/tmp/tmp035k5jyg/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-23 06:59:07,006 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 06:59:07,008 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt 2021-09-23 06:59:07,008 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-23 06:59:07,009 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 06:59:07,009 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 06:59:07,009 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-23 06:59:07,009 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/SRR7500318/__temp__/aligned/inter.pairs.txt" "/tmp/tmptfjlja9_/inter_no_balanced.cool" 2021-09-23 07:00:07,377 INFO SimpleSubprocess MakeCool - 0:01:00 2021-09-23 07:00:07,377 DEBUG SimpleSubprocess cp "/tmp/tmptfjlja9_/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-23 07:00:07,397 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:00:07,399 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt 2021-09-23 07:00:07,399 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-23 07:00:07,400 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 07:00:07,400 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 07:00:07,400 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-23 07:00:07,421 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/SRR7500318/__temp__/aligned/inter.pairs.txt" "/tmp/tmp0dg54b56/inter_no_balanced.cool" 2021-09-23 07:01:05,195 INFO SimpleSubprocess MakeCool - 0:00:57 2021-09-23 07:01:05,195 DEBUG SimpleSubprocess cp "/tmp/tmp0dg54b56/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-23 07:01:05,212 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:01:05,216 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-23 07:01:05,216 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_5kb.cool 2021-09-23 07:01:05,216 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 07:01:05,216 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp5iabpdeh/inter.cool" 2021-09-23 07:01:05,243 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 07:01:05,243 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp5iabpdeh/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 07:01:26,376 INFO SimpleSubprocess NormalizeCool - 0:00:21 2021-09-23 07:01:26,376 DEBUG SimpleSubprocess cp "/tmp/tmp5iabpdeh/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_5kb.cool" 2021-09-23 07:01:26,404 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:01:26,407 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-23 07:01:26,407 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_10kb.cool 2021-09-23 07:01:26,407 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 07:01:26,449 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpv2xwyar4/inter.cool" 2021-09-23 07:01:26,472 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 07:01:26,472 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpv2xwyar4/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 07:01:30,090 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-23 07:01:30,090 DEBUG SimpleSubprocess cp "/tmp/tmpv2xwyar4/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_10kb.cool" 2021-09-23 07:01:30,114 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:01:30,117 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-23 07:01:30,117 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_20kb.cool 2021-09-23 07:01:30,117 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 07:01:30,117 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp8fsvav1y/inter.cool" 2021-09-23 07:01:30,137 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 07:01:30,138 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp8fsvav1y/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 07:01:33,008 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-23 07:01:33,008 DEBUG SimpleSubprocess cp "/tmp/tmp8fsvav1y/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_20kb.cool" 2021-09-23 07:01:33,029 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:01:33,032 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-23 07:01:33,032 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_25kb.cool 2021-09-23 07:01:33,032 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 07:01:33,033 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpdplinwzc/inter.cool" 2021-09-23 07:01:33,052 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 07:01:33,052 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpdplinwzc/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 07:01:35,732 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-23 07:01:35,733 DEBUG SimpleSubprocess cp "/tmp/tmpdplinwzc/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_25kb.cool" 2021-09-23 07:01:35,752 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:01:35,755 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-23 07:01:35,755 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_50kb.cool 2021-09-23 07:01:35,755 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 07:01:35,773 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpm1xkbhmu/inter.cool" 2021-09-23 07:01:35,791 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 07:01:35,791 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpm1xkbhmu/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 07:01:37,655 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-23 07:01:37,655 DEBUG SimpleSubprocess cp "/tmp/tmpm1xkbhmu/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_50kb.cool" 2021-09-23 07:01:37,673 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:01:37,677 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt 2021-09-23 07:01:37,683 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-23 07:01:37,683 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_5kb.cool 2021-09-23 07:01:37,683 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt 2021-09-23 07:01:37,684 INFO AddWeight Chromosome: chr1 2021-09-23 07:01:37,684 INFO AddWeight Resolution [bp]: 5000 2021-09-23 07:01:37,783 INFO AddWeight AddWeight successfully finished 2021-09-23 07:01:37,783 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_10kb.cool 2021-09-23 07:01:37,783 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt 2021-09-23 07:01:37,784 INFO AddWeight Chromosome: chr1 2021-09-23 07:01:37,784 INFO AddWeight Resolution [bp]: 10000 2021-09-23 07:01:37,858 INFO AddWeight AddWeight successfully finished 2021-09-23 07:01:37,859 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_20kb.cool 2021-09-23 07:01:37,859 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt 2021-09-23 07:01:37,859 INFO AddWeight Chromosome: chr1 2021-09-23 07:01:37,859 INFO AddWeight Resolution [bp]: 20000 2021-09-23 07:01:37,903 INFO AddWeight AddWeight successfully finished 2021-09-23 07:01:37,903 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_25kb.cool 2021-09-23 07:01:37,903 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt 2021-09-23 07:01:37,903 INFO AddWeight Chromosome: chr1 2021-09-23 07:01:37,903 INFO AddWeight Resolution [bp]: 25000 2021-09-23 07:01:37,942 INFO AddWeight AddWeight successfully finished 2021-09-23 07:01:37,942 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_50kb.cool 2021-09-23 07:01:37,942 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt 2021-09-23 07:01:37,942 INFO AddWeight Chromosome: chr1 2021-09-23 07:01:37,943 INFO AddWeight Resolution [bp]: 50000 2021-09-23 07:01:37,970 INFO AddWeight AddWeight successfully finished 2021-09-23 07:01:37,971 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.hic 2021-09-23 07:01:37,972 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_norm.hic 2021-09-23 07:01:37,972 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt 2021-09-23 07:01:37,972 INFO Vector2HiC Threads: 10 2021-09-23 07:01:38,005 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.hic" "/tmp/tmpkdmbuc9r/inter.hic" 2021-09-23 07:01:38,261 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 07:01:38,261 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-09-23 07:01:38,262 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkdmbuc9r/inter.hic" "/tmp/tmpkdmbuc9r/vector.txt" 2021-09-23 07:01:43,269 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-23 07:01:43,269 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-09-23 07:01:43,287 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkdmbuc9r/inter.hic" "/tmp/tmpkdmbuc9r/vector.txt" 2021-09-23 07:01:47,546 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-23 07:01:47,546 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-09-23 07:01:47,547 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkdmbuc9r/inter.hic" "/tmp/tmpkdmbuc9r/vector.txt" 2021-09-23 07:01:51,214 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 07:01:51,215 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-09-23 07:01:51,215 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkdmbuc9r/inter.hic" "/tmp/tmpkdmbuc9r/vector.txt" 2021-09-23 07:01:55,132 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 07:01:55,133 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-09-23 07:01:55,145 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkdmbuc9r/inter.hic" "/tmp/tmpkdmbuc9r/vector.txt" 2021-09-23 07:01:58,830 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 07:01:58,831 DEBUG SimpleSubprocess cp "/tmp/tmpkdmbuc9r/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_norm.hic" 2021-09-23 07:01:59,160 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 07:01:59,212 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/merged_nodups.txt" 2021-09-23 07:02:16,348 INFO SimpleSubprocess CopyResult - 0:00:17 2021-09-23 07:02:16,349 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter.pairs.txt" 2021-09-23 07:02:27,276 INFO SimpleSubprocess CopyResult - 0:00:10 2021-09-23 07:02:27,276 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/vector.txt" 2021-09-23 07:02:27,286 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:27,286 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter.hic" 2021-09-23 07:02:29,836 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-23 07:02:29,836 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_statistics.txt" 2021-09-23 07:02:29,844 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:29,844 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_no_balanced_5kb.cool" 2021-09-23 07:02:30,008 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,008 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_5kb.cool" 2021-09-23 07:02:30,172 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,172 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_no_balanced_10kb.cool" 2021-09-23 07:02:30,319 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,319 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_10kb.cool" 2021-09-23 07:02:30,452 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,452 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_no_balanced_20kb.cool" 2021-09-23 07:02:30,567 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,567 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_20kb.cool" 2021-09-23 07:02:30,683 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,683 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_no_balanced_25kb.cool" 2021-09-23 07:02:30,784 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,784 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_25kb.cool" 2021-09-23 07:02:30,883 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,883 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_no_balanced_50kb.cool" 2021-09-23 07:02:30,967 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:30,968 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/inter_50kb.cool" 2021-09-23 07:02:31,051 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 07:02:31,427 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500318/__temp__" 2021-09-23 07:02:38,824 INFO SimpleSubprocess RemoveTemp - 0:00:07 2021-09-23 07:02:38,824 INFO BenchmarkPipeline 'SRR7500318' FINISHED, SUMMARY TIME - 7:06:35