2021-09-20 11:28:38,909 INFO BenchmarkPipeline --- START PROCESSING 'SRR6158160-SRR6158161' --- 2021-09-20 11:28:38,909 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158160.sra 2021-09-20 11:28:38,909 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__ 2021-09-20 11:28:38,910 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpcg6dnciy "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158160.sra" 2021-09-20 12:11:19,151 INFO SimpleSubprocess Sra2FastQ - 0:42:40 2021-09-20 12:11:19,186 DEBUG SimpleSubprocess gzip /tmp/tmpcg6dnciy/* 2021-09-20 15:29:35,655 INFO SimpleSubprocess GZipFastQ - 3:18:16 2021-09-20 15:29:35,695 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/fastq"; mv /tmp/tmpcg6dnciy/SRR6158160_1.fastq.gz /tmp/tmpcg6dnciy/SRR6158160_R1.fastq.gz; mv /tmp/tmpcg6dnciy/SRR6158160_2.fastq.gz /tmp/tmpcg6dnciy/SRR6158160_R2.fastq.gz; cp /tmp/tmpcg6dnciy/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/fastq" 2021-09-20 15:38:07,092 INFO SimpleSubprocess CopyFiles - 0:08:31 2021-09-20 15:38:10,080 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158161.sra 2021-09-20 15:38:10,080 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__ 2021-09-20 15:38:10,080 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp0mv0y7yb "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158161.sra" 2021-09-20 16:14:39,483 INFO SimpleSubprocess Sra2FastQ - 0:36:29 2021-09-20 16:14:39,503 DEBUG SimpleSubprocess gzip /tmp/tmp0mv0y7yb/* 2021-09-20 19:28:31,102 INFO SimpleSubprocess GZipFastQ - 3:13:51 2021-09-20 19:28:31,113 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/fastq"; mv /tmp/tmp0mv0y7yb/SRR6158161_1.fastq.gz /tmp/tmp0mv0y7yb/SRR6158161_R1.fastq.gz; mv /tmp/tmp0mv0y7yb/SRR6158161_2.fastq.gz /tmp/tmp0mv0y7yb/SRR6158161_R2.fastq.gz; cp /tmp/tmp0mv0y7yb/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/fastq" 2021-09-20 19:35:23,994 INFO SimpleSubprocess CopyFiles - 0:06:52 2021-09-20 19:35:26,323 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__ 2021-09-20 19:35:26,323 INFO Juicer Genome assembly: mm10 2021-09-20 19:35:26,323 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-20 19:35:26,323 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-20 19:35:26,323 INFO Juicer Enzyme: HindIII 2021-09-20 19:35:26,323 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt 2021-09-20 19:35:26,323 INFO Juicer Threads: 10 2021-09-20 19:35:26,323 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/HIC_tmp" 2021-09-20 19:35:26,366 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-20 19:35:26,367 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 HindIII -y "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt" -d "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__" 2021-09-21 23:28:47,882 INFO SimpleSubprocess Juicer - 1 day, 3:53:21 2021-09-21 23:28:48,302 INFO Juicer Using /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt as site file (-: Looking for fastq files...fastq files exist (-: Aligning files matching /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/fastq/*_R*.fastq* to genome mm10 with site file /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt (-: Created /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158160_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158160_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158160.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158160.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158161_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158161_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158161.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/splits/SRR6158161.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 [2021-09-21T16:06:48,990] [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 [2021-09-21T20:19:15,676] [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/SRR6158160-SRR6158161/__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 [2021-09-21T23:15:11,587] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_30.hic Using 1 CPU thread(s) Default settings for 10kb being used max 21.0 4% 9% 14% 19% 23% 28% 33% 38% 42% 47% 52% 57% 61% 66% 71% 76% 80% 85% 90% 95% 100% 1641 features written to file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_30_contact_domains/10000_blocks.bedpe 1641 domains written to file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_30_contact_domains/10000_blocks.bedpe Arrowhead complete 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/SRR6158160-SRR6158161/__temp__/aligned for results 2021-09-21 23:28:48,640 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/merged_nodups.txt 2021-09-21 23:28:48,640 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt 2021-09-21 23:28:48,901 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp7a6wpxif/inter.pairs.txt" 2021-09-21 23:39:12,833 INFO SimpleSubprocess MakeInterPairs - 0:10:23 2021-09-21 23:39:12,850 DEBUG SimpleSubprocess cp "/tmp/tmp7a6wpxif/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt" 2021-09-21 23:39:30,624 INFO SimpleSubprocess CopyFiles - 0:00:17 2021-09-21 23:39:32,567 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt 2021-09-21 23:39:32,568 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-21 23:39:32,568 INFO Pairs2Cool Genome assembly: mm10 2021-09-21 23:39:32,568 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-21 23:39:32,568 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-21 23:39:32,589 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/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt" "/tmp/tmpyf8mobn_/inter_no_balanced.cool" 2021-09-21 23:49:56,147 INFO SimpleSubprocess MakeCool - 0:10:23 2021-09-21 23:49:56,147 DEBUG SimpleSubprocess cp "/tmp/tmpyf8mobn_/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-21 23:49:56,391 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-21 23:49:56,446 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt 2021-09-21 23:49:56,446 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-21 23:49:56,446 INFO Pairs2Cool Genome assembly: mm10 2021-09-21 23:49:56,446 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-21 23:49:56,446 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-21 23:49:56,446 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/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt" "/tmp/tmp340ot3ws/inter_no_balanced.cool" 2021-09-21 23:59:25,002 INFO SimpleSubprocess MakeCool - 0:09:28 2021-09-21 23:59:25,002 DEBUG SimpleSubprocess cp "/tmp/tmp340ot3ws/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-21 23:59:25,225 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-21 23:59:25,282 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt 2021-09-21 23:59:25,282 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-21 23:59:25,282 INFO Pairs2Cool Genome assembly: mm10 2021-09-21 23:59:25,282 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-21 23:59:25,282 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-21 23:59:25,342 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/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt" "/tmp/tmps3029ql3/inter_no_balanced.cool" 2021-09-22 00:08:11,246 INFO SimpleSubprocess MakeCool - 0:08:45 2021-09-22 00:08:11,246 DEBUG SimpleSubprocess cp "/tmp/tmps3029ql3/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-22 00:08:11,417 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:08:11,440 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt 2021-09-22 00:08:11,440 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-22 00:08:11,440 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 00:08:11,441 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 00:08:11,441 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-22 00:08:11,514 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/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt" "/tmp/tmpp1at1jl2/inter_no_balanced.cool" 2021-09-22 00:16:41,596 INFO SimpleSubprocess MakeCool - 0:08:30 2021-09-22 00:16:41,596 DEBUG SimpleSubprocess cp "/tmp/tmpp1at1jl2/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-22 00:16:41,745 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:16:41,792 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt 2021-09-22 00:16:41,792 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-22 00:16:41,792 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 00:16:41,792 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 00:16:41,792 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-22 00:16:41,816 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/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt" "/tmp/tmpffo4il6s/inter_no_balanced.cool" 2021-09-22 00:24:39,981 INFO SimpleSubprocess MakeCool - 0:07:58 2021-09-22 00:24:40,008 DEBUG SimpleSubprocess cp "/tmp/tmpffo4il6s/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-22 00:24:40,137 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:24:40,212 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-22 00:24:40,212 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_5kb.cool 2021-09-22 00:24:40,212 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-22 00:24:40,212 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpxs6n5atg/inter.cool" 2021-09-22 00:24:40,475 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 00:24:40,475 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpxs6n5atg/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-22 00:24:46,435 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-22 00:24:46,436 DEBUG SimpleSubprocess cp "/tmp/tmpxs6n5atg/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_5kb.cool" 2021-09-22 00:24:46,693 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:24:46,759 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-22 00:24:46,759 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_10kb.cool 2021-09-22 00:24:46,759 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-22 00:24:46,759 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp0yvs019_/inter.cool" 2021-09-22 00:24:46,978 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 00:24:46,978 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp0yvs019_/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-22 00:24:50,033 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-22 00:24:50,034 DEBUG SimpleSubprocess cp "/tmp/tmp0yvs019_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_10kb.cool" 2021-09-22 00:24:50,229 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:24:50,282 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-22 00:24:50,283 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_20kb.cool 2021-09-22 00:24:50,283 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-22 00:24:50,307 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpyoxv8h32/inter.cool" 2021-09-22 00:24:50,491 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 00:24:50,492 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpyoxv8h32/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-22 00:24:52,934 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-22 00:24:52,935 DEBUG SimpleSubprocess cp "/tmp/tmpyoxv8h32/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_20kb.cool" 2021-09-22 00:24:53,115 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:24:53,162 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-22 00:24:53,162 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_25kb.cool 2021-09-22 00:24:53,162 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-22 00:24:53,186 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmppglzec44/inter.cool" 2021-09-22 00:24:53,351 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 00:24:53,351 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmppglzec44/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-22 00:24:55,647 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-22 00:24:55,647 DEBUG SimpleSubprocess cp "/tmp/tmppglzec44/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_25kb.cool" 2021-09-22 00:24:55,808 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:24:55,853 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-22 00:24:55,854 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_50kb.cool 2021-09-22 00:24:55,854 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-22 00:24:55,878 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp3tb5trsi/inter.cool" 2021-09-22 00:24:56,007 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 00:24:56,007 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3tb5trsi/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-22 00:24:57,883 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-22 00:24:57,883 DEBUG SimpleSubprocess cp "/tmp/tmp3tb5trsi/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_50kb.cool" 2021-09-22 00:24:58,011 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 00:24:58,032 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt 2021-09-22 00:24:58,038 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-22 00:24:58,095 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_5kb.cool 2021-09-22 00:24:58,095 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt 2021-09-22 00:24:58,095 INFO AddWeight Chromosome: chrX 2021-09-22 00:24:58,095 INFO AddWeight Resolution [bp]: 5000 2021-09-22 00:25:04,319 INFO AddWeight AddWeight successfully finished 2021-09-22 00:25:04,320 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_10kb.cool 2021-09-22 00:25:04,320 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt 2021-09-22 00:25:04,320 INFO AddWeight Chromosome: chrX 2021-09-22 00:25:04,320 INFO AddWeight Resolution [bp]: 10000 2021-09-22 00:25:04,390 INFO AddWeight AddWeight successfully finished 2021-09-22 00:25:04,390 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_20kb.cool 2021-09-22 00:25:04,390 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt 2021-09-22 00:25:04,390 INFO AddWeight Chromosome: chrX 2021-09-22 00:25:04,390 INFO AddWeight Resolution [bp]: 20000 2021-09-22 00:25:04,432 INFO AddWeight AddWeight successfully finished 2021-09-22 00:25:04,432 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_25kb.cool 2021-09-22 00:25:04,432 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt 2021-09-22 00:25:04,432 INFO AddWeight Chromosome: chrX 2021-09-22 00:25:04,432 INFO AddWeight Resolution [bp]: 25000 2021-09-22 00:25:04,469 INFO AddWeight AddWeight successfully finished 2021-09-22 00:25:04,469 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_50kb.cool 2021-09-22 00:25:04,469 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt 2021-09-22 00:25:04,469 INFO AddWeight Chromosome: chrX 2021-09-22 00:25:04,469 INFO AddWeight Resolution [bp]: 50000 2021-09-22 00:25:04,495 INFO AddWeight AddWeight successfully finished 2021-09-22 00:25:04,498 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.hic 2021-09-22 00:25:04,498 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_norm.hic 2021-09-22 00:25:04,498 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt 2021-09-22 00:25:04,498 INFO Vector2HiC Threads: 10 2021-09-22 00:25:04,537 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.hic" "/tmp/tmpsky7kvkd/inter.hic" 2021-09-22 00:25:10,329 INFO SimpleSubprocess TempFiles - 0:00:05 2021-09-22 00:25:10,330 INFO Vector2HiC Vector: vector c-tale_normalization chrX 5000 BP 2021-09-22 00:25:10,331 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsky7kvkd/inter.hic" "/tmp/tmpsky7kvkd/vector.txt" 2021-09-22 00:25:17,130 INFO SimpleSubprocess NormalizeHiC - 0:00:06 2021-09-22 00:25:17,131 INFO Vector2HiC Vector: vector c-tale_normalization chrX 10000 BP 2021-09-22 00:25:17,132 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsky7kvkd/inter.hic" "/tmp/tmpsky7kvkd/vector.txt" 2021-09-22 00:25:22,237 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-22 00:25:22,238 INFO Vector2HiC Vector: vector c-tale_normalization chrX 20000 BP 2021-09-22 00:25:22,282 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsky7kvkd/inter.hic" "/tmp/tmpsky7kvkd/vector.txt" 2021-09-22 00:25:26,441 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-22 00:25:26,441 INFO Vector2HiC Vector: vector c-tale_normalization chrX 25000 BP 2021-09-22 00:25:26,459 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsky7kvkd/inter.hic" "/tmp/tmpsky7kvkd/vector.txt" 2021-09-22 00:25:30,730 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-22 00:25:30,730 INFO Vector2HiC Vector: vector c-tale_normalization chrX 50000 BP 2021-09-22 00:25:30,854 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsky7kvkd/inter.hic" "/tmp/tmpsky7kvkd/vector.txt" 2021-09-22 00:25:35,322 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-22 00:25:35,322 DEBUG SimpleSubprocess cp "/tmp/tmpsky7kvkd/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_norm.hic" 2021-09-22 00:25:37,023 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-22 00:25:37,791 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/merged_nodups.txt" 2021-09-22 00:46:35,015 INFO SimpleSubprocess CopyResult - 0:20:57 2021-09-22 00:46:35,032 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter.pairs.txt" 2021-09-22 00:47:42,991 INFO SimpleSubprocess CopyResult - 0:01:07 2021-09-22 00:47:42,991 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/vector.txt" 2021-09-22 00:47:43,056 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 00:47:43,056 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter.hic" 2021-09-22 00:48:03,225 INFO SimpleSubprocess CopyResult - 0:00:20 2021-09-22 00:48:03,226 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_statistics.txt" 2021-09-22 00:48:03,250 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 00:48:03,250 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_no_balanced_5kb.cool" 2021-09-22 00:48:05,504 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-22 00:48:05,504 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_5kb.cool" 2021-09-22 00:48:07,930 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-22 00:48:07,931 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_no_balanced_10kb.cool" 2021-09-22 00:48:10,232 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-22 00:48:10,232 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_10kb.cool" 2021-09-22 00:48:12,205 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-22 00:48:12,206 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_no_balanced_20kb.cool" 2021-09-22 00:48:14,683 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-22 00:48:14,683 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_20kb.cool" 2021-09-22 00:48:16,387 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-22 00:48:16,388 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_no_balanced_25kb.cool" 2021-09-22 00:48:17,682 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-22 00:48:17,682 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_25kb.cool" 2021-09-22 00:48:19,277 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-22 00:48:19,277 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_no_balanced_50kb.cool" 2021-09-22 00:48:20,578 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-22 00:48:20,578 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/inter_50kb.cool" 2021-09-22 00:48:21,857 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-22 00:48:21,957 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158160-SRR6158161/__temp__" 2021-09-22 00:49:12,723 INFO SimpleSubprocess RemoveTemp - 0:00:50 2021-09-22 00:49:12,723 INFO BenchmarkPipeline 'SRR6158160-SRR6158161' FINISHED, SUMMARY TIME - 1 day, 13:20:33