2021-09-30 03:34:49,221 INFO BenchmarkPipeline --- START PROCESSING 'SRR8984912' --- 2021-09-30 03:34:49,221 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984912.sra 2021-09-30 03:34:49,221 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__ 2021-09-30 03:34:49,221 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp38bihnqq "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984912.sra" 2021-09-30 03:54:46,988 INFO SimpleSubprocess Sra2FastQ - 0:19:57 2021-09-30 03:54:47,010 DEBUG SimpleSubprocess gzip /tmp/tmp38bihnqq/* 2021-09-30 04:55:18,846 INFO SimpleSubprocess GZipFastQ - 1:00:31 2021-09-30 04:55:18,855 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/fastq"; mv /tmp/tmp38bihnqq/SRR8984912_1.fastq.gz /tmp/tmp38bihnqq/SRR8984912_R1.fastq.gz; mv /tmp/tmp38bihnqq/SRR8984912_2.fastq.gz /tmp/tmp38bihnqq/SRR8984912_R2.fastq.gz; cp /tmp/tmp38bihnqq/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/fastq" 2021-09-30 04:55:45,517 INFO SimpleSubprocess CopyFiles - 0:00:26 2021-09-30 04:55:47,052 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__ 2021-09-30 04:55:47,052 INFO Juicer Genome assembly: mm10 2021-09-30 04:55:47,052 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-30 04:55:47,052 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 04:55:47,052 INFO Juicer Enzyme: DpnII 2021-09-30 04:55:47,052 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-30 04:55:47,052 INFO Juicer Threads: 10 2021-09-30 04:55:47,052 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/HIC_tmp" 2021-09-30 04:55:47,106 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-30 04:55:47,106 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/SRR8984912/__temp__" 2021-09-30 09:59:13,024 INFO SimpleSubprocess Juicer - 5:03:25 2021-09-30 09:59:13,056 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/SRR8984912/__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/SRR8984912/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/splits/SRR8984912_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/splits/SRR8984912_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/splits/SRR8984912.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/splits/SRR8984912.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 [2021-09-30T09:24:50,762] [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 [2021-09-30T09:44:25,047] [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/SRR8984912/__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 [2021-09-30T09:59:12,594] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__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/SRR8984912/__temp__/aligned for results 2021-09-30 09:59:13,140 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/merged_nodups.txt 2021-09-30 09:59:13,140 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt 2021-09-30 09:59:13,168 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpcwm31he8/inter.pairs.txt" 2021-09-30 09:59:50,354 INFO SimpleSubprocess MakeInterPairs - 0:00:37 2021-09-30 09:59:50,354 DEBUG SimpleSubprocess cp "/tmp/tmpcwm31he8/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt" 2021-09-30 09:59:51,311 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 09:59:51,439 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt 2021-09-30 09:59:51,439 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-30 09:59:51,439 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 09:59:51,440 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 09:59:51,440 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-30 09:59:51,440 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/SRR8984912/__temp__/aligned/inter.pairs.txt" "/tmp/tmptvnnhxa0/inter_no_balanced.cool" 2021-09-30 10:00:55,751 INFO SimpleSubprocess MakeCool - 0:01:04 2021-09-30 10:00:55,751 DEBUG SimpleSubprocess cp "/tmp/tmptvnnhxa0/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-30 10:00:55,826 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:00:55,829 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt 2021-09-30 10:00:55,829 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-30 10:00:55,829 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 10:00:55,829 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 10:00:55,829 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-30 10:00:55,835 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/SRR8984912/__temp__/aligned/inter.pairs.txt" "/tmp/tmpu5fydf2n/inter_no_balanced.cool" 2021-09-30 10:01:49,254 INFO SimpleSubprocess MakeCool - 0:00:53 2021-09-30 10:01:49,254 DEBUG SimpleSubprocess cp "/tmp/tmpu5fydf2n/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-30 10:01:49,277 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:01:49,279 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt 2021-09-30 10:01:49,279 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-30 10:01:49,279 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 10:01:49,279 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 10:01:49,280 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-30 10:01:49,280 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/SRR8984912/__temp__/aligned/inter.pairs.txt" "/tmp/tmpmcaiezk9/inter_no_balanced.cool" 2021-09-30 10:02:39,271 INFO SimpleSubprocess MakeCool - 0:00:49 2021-09-30 10:02:39,271 DEBUG SimpleSubprocess cp "/tmp/tmpmcaiezk9/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-30 10:02:39,291 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:02:39,293 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt 2021-09-30 10:02:39,293 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-30 10:02:39,293 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 10:02:39,294 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 10:02:39,294 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-30 10:02:39,294 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/SRR8984912/__temp__/aligned/inter.pairs.txt" "/tmp/tmpe7x5dd7d/inter_no_balanced.cool" 2021-09-30 10:03:28,849 INFO SimpleSubprocess MakeCool - 0:00:49 2021-09-30 10:03:28,849 DEBUG SimpleSubprocess cp "/tmp/tmpe7x5dd7d/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-30 10:03:28,868 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:03:28,901 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt 2021-09-30 10:03:28,901 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-30 10:03:28,901 INFO Pairs2Cool Genome assembly: mm10 2021-09-30 10:03:28,901 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-30 10:03:28,901 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-30 10:03:28,908 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/SRR8984912/__temp__/aligned/inter.pairs.txt" "/tmp/tmpgssrd36b/inter_no_balanced.cool" 2021-09-30 10:04:15,544 INFO SimpleSubprocess MakeCool - 0:00:46 2021-09-30 10:04:15,544 DEBUG SimpleSubprocess cp "/tmp/tmpgssrd36b/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-30 10:04:15,562 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:04:15,566 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-30 10:04:15,566 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_5kb.cool 2021-09-30 10:04:15,566 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 10:04:15,578 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp0isppfpn/inter.cool" 2021-09-30 10:04:15,603 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 10:04:15,603 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp0isppfpn/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 10:04:27,730 INFO SimpleSubprocess NormalizeCool - 0:00:12 2021-09-30 10:04:27,730 DEBUG SimpleSubprocess cp "/tmp/tmp0isppfpn/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_5kb.cool" 2021-09-30 10:04:27,757 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:04:27,785 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-30 10:04:27,785 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_10kb.cool 2021-09-30 10:04:27,785 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 10:04:27,815 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpqj5vxecv/inter.cool" 2021-09-30 10:04:27,837 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 10:04:27,837 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpqj5vxecv/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 10:04:35,965 INFO SimpleSubprocess NormalizeCool - 0:00:08 2021-09-30 10:04:35,965 DEBUG SimpleSubprocess cp "/tmp/tmpqj5vxecv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_10kb.cool" 2021-09-30 10:04:35,988 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:04:35,991 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-30 10:04:35,991 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_20kb.cool 2021-09-30 10:04:35,991 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 10:04:36,015 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpbx02vkiq/inter.cool" 2021-09-30 10:04:36,035 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 10:04:36,035 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpbx02vkiq/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 10:04:41,466 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-30 10:04:41,466 DEBUG SimpleSubprocess cp "/tmp/tmpbx02vkiq/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_20kb.cool" 2021-09-30 10:04:41,487 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:04:41,489 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-30 10:04:41,489 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_25kb.cool 2021-09-30 10:04:41,489 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 10:04:41,513 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpfj_b3oo9/inter.cool" 2021-09-30 10:04:41,532 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 10:04:41,532 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpfj_b3oo9/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 10:04:46,383 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-30 10:04:46,384 DEBUG SimpleSubprocess cp "/tmp/tmpfj_b3oo9/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_25kb.cool" 2021-09-30 10:04:46,403 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:04:46,436 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-30 10:04:46,436 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_50kb.cool 2021-09-30 10:04:46,436 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-30 10:04:46,437 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp7xl_9et9/inter.cool" 2021-09-30 10:04:46,454 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 10:04:46,454 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp7xl_9et9/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-30 10:04:49,519 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-30 10:04:49,519 DEBUG SimpleSubprocess cp "/tmp/tmp7xl_9et9/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_50kb.cool" 2021-09-30 10:04:49,536 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:04:49,540 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt 2021-09-30 10:04:49,547 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-30 10:04:49,547 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_5kb.cool 2021-09-30 10:04:49,547 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt 2021-09-30 10:04:49,547 INFO AddWeight Chromosome: chr5 2021-09-30 10:04:49,547 INFO AddWeight Resolution [bp]: 5000 2021-09-30 10:04:50,387 INFO AddWeight AddWeight successfully finished 2021-09-30 10:04:50,387 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_10kb.cool 2021-09-30 10:04:50,387 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt 2021-09-30 10:04:50,387 INFO AddWeight Chromosome: chr5 2021-09-30 10:04:50,387 INFO AddWeight Resolution [bp]: 10000 2021-09-30 10:04:50,426 INFO AddWeight AddWeight successfully finished 2021-09-30 10:04:50,427 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_20kb.cool 2021-09-30 10:04:50,427 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt 2021-09-30 10:04:50,427 INFO AddWeight Chromosome: chr5 2021-09-30 10:04:50,427 INFO AddWeight Resolution [bp]: 20000 2021-09-30 10:04:50,453 INFO AddWeight AddWeight successfully finished 2021-09-30 10:04:50,453 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_25kb.cool 2021-09-30 10:04:50,453 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt 2021-09-30 10:04:50,453 INFO AddWeight Chromosome: chr5 2021-09-30 10:04:50,453 INFO AddWeight Resolution [bp]: 25000 2021-09-30 10:04:50,483 INFO AddWeight AddWeight successfully finished 2021-09-30 10:04:50,483 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_50kb.cool 2021-09-30 10:04:50,483 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt 2021-09-30 10:04:50,483 INFO AddWeight Chromosome: chr5 2021-09-30 10:04:50,483 INFO AddWeight Resolution [bp]: 50000 2021-09-30 10:04:50,501 INFO AddWeight AddWeight successfully finished 2021-09-30 10:04:50,503 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.hic 2021-09-30 10:04:50,503 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_norm.hic 2021-09-30 10:04:50,503 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt 2021-09-30 10:04:50,504 INFO Vector2HiC Threads: 10 2021-09-30 10:04:50,525 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.hic" "/tmp/tmpmikymqx5/inter.hic" 2021-09-30 10:04:50,780 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-30 10:04:50,780 INFO Vector2HiC Vector: vector c-tale_normalization chr5 5000 BP 2021-09-30 10:04:50,781 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpmikymqx5/inter.hic" "/tmp/tmpmikymqx5/vector.txt" 2021-09-30 10:04:55,263 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-30 10:04:55,263 INFO Vector2HiC Vector: vector c-tale_normalization chr5 10000 BP 2021-09-30 10:04:55,264 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpmikymqx5/inter.hic" "/tmp/tmpmikymqx5/vector.txt" 2021-09-30 10:04:59,058 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-30 10:04:59,058 INFO Vector2HiC Vector: vector c-tale_normalization chr5 20000 BP 2021-09-30 10:04:59,059 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpmikymqx5/inter.hic" "/tmp/tmpmikymqx5/vector.txt" 2021-09-30 10:05:02,664 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-30 10:05:02,664 INFO Vector2HiC Vector: vector c-tale_normalization chr5 25000 BP 2021-09-30 10:05:02,664 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpmikymqx5/inter.hic" "/tmp/tmpmikymqx5/vector.txt" 2021-09-30 10:05:06,356 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-30 10:05:06,356 INFO Vector2HiC Vector: vector c-tale_normalization chr5 50000 BP 2021-09-30 10:05:06,356 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpmikymqx5/inter.hic" "/tmp/tmpmikymqx5/vector.txt" 2021-09-30 10:05:10,037 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-30 10:05:10,037 DEBUG SimpleSubprocess cp "/tmp/tmpmikymqx5/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_norm.hic" 2021-09-30 10:05:10,370 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-30 10:05:10,442 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/merged_nodups.txt" 2021-09-30 10:05:26,088 INFO SimpleSubprocess CopyResult - 0:00:15 2021-09-30 10:05:26,089 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter.pairs.txt" 2021-09-30 10:05:32,147 INFO SimpleSubprocess CopyResult - 0:00:06 2021-09-30 10:05:32,147 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/vector.txt" 2021-09-30 10:05:32,156 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:32,156 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter.hic" 2021-09-30 10:05:35,090 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-30 10:05:35,091 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_statistics.txt" 2021-09-30 10:05:35,099 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:35,099 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_no_balanced_5kb.cool" 2021-09-30 10:05:35,263 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:35,264 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_5kb.cool" 2021-09-30 10:05:35,594 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:35,595 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_no_balanced_10kb.cool" 2021-09-30 10:05:35,687 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:35,688 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_10kb.cool" 2021-09-30 10:05:35,780 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:35,780 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_no_balanced_20kb.cool" 2021-09-30 10:05:35,876 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:35,876 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_20kb.cool" 2021-09-30 10:05:35,948 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:35,949 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_no_balanced_25kb.cool" 2021-09-30 10:05:36,043 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:36,043 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_25kb.cool" 2021-09-30 10:05:36,131 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:36,132 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_no_balanced_50kb.cool" 2021-09-30 10:05:36,188 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:36,188 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/inter_50kb.cool" 2021-09-30 10:05:36,244 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-30 10:05:36,265 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984912/__temp__" 2021-09-30 10:05:47,188 INFO SimpleSubprocess RemoveTemp - 0:00:10 2021-09-30 10:05:47,189 INFO BenchmarkPipeline 'SRR8984912' FINISHED, SUMMARY TIME - 6:30:57