2021-08-31 03:30:43,985 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099910' --- 2021-08-31 03:30:43,989 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099910.sra 2021-08-31 03:30:43,989 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__ 2021-08-31 03:30:43,990 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpbcxyg3bm "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099910.sra" 2021-08-31 04:16:33,983 INFO SimpleSubprocess Sra2FastQ - 0:45:49 2021-08-31 04:16:34,000 DEBUG SimpleSubprocess gzip /tmp/tmpbcxyg3bm/* 2021-08-31 07:37:14,218 INFO SimpleSubprocess GZipFastQ - 3:20:39 2021-08-31 07:37:15,780 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/fastq"; mv /tmp/tmpbcxyg3bm/SRR5099910_1.fastq.gz /tmp/tmpbcxyg3bm/SRR5099910_R1.fastq.gz; mv /tmp/tmpbcxyg3bm/SRR5099910_2.fastq.gz /tmp/tmpbcxyg3bm/SRR5099910_R2.fastq.gz; cp /tmp/tmpbcxyg3bm/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/fastq" 2021-08-31 07:44:14,155 INFO SimpleSubprocess CopyFiles - 0:06:58 2021-08-31 07:44:19,542 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__ 2021-08-31 07:44:19,543 INFO Juicer Genome assembly: mm10 2021-08-31 07:44:19,543 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-31 07:44:19,543 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 07:44:19,543 INFO Juicer Enzyme: DpnII 2021-08-31 07:44:19,543 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-31 07:44:19,574 INFO Juicer Threads: 10 2021-08-31 07:44:19,662 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/SRR5099910/__temp__" 2021-08-31 19:08:40,924 INFO SimpleSubprocess Juicer - 11:24:21 2021-08-31 19:08:41,235 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/SRR5099910/__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/SRR5099910/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/splits/SRR5099910_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/splits/SRR5099910_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/splits/SRR5099910.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/splits/SRR5099910.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 [2021-08-31T17:41:03,753] [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 [2021-08-31T18:24:48,081] [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/SRR5099910/__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 [2021-08-31T19:08:37,742] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__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/SRR5099910/__temp__/aligned for results 2021-08-31 19:08:41,609 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/merged_nodups.txt 2021-08-31 19:08:41,616 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt 2021-08-31 19:08:41,848 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpz2d2vezn/inter.pairs.txt" 2021-08-31 19:09:50,768 INFO SimpleSubprocess MakeInterPairs - 0:01:08 2021-08-31 19:09:50,769 DEBUG SimpleSubprocess cp "/tmp/tmpz2d2vezn/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt" 2021-08-31 19:09:52,441 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-31 19:09:52,914 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt 2021-08-31 19:09:52,915 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-31 19:09:52,915 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 19:09:52,915 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 19:09:52,915 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-31 19:09:52,967 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/SRR5099910/__temp__/aligned/inter.pairs.txt" "/tmp/tmplf8q7506/inter_no_balanced.cool" 2021-08-31 19:11:29,022 INFO SimpleSubprocess MakeCool - 0:01:36 2021-08-31 19:11:29,022 DEBUG SimpleSubprocess cp "/tmp/tmplf8q7506/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-31 19:11:29,056 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:11:29,217 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt 2021-08-31 19:11:29,217 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-31 19:11:29,217 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 19:11:29,217 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 19:11:29,217 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-31 19:11:29,309 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/SRR5099910/__temp__/aligned/inter.pairs.txt" "/tmp/tmpip79d7tr/inter_no_balanced.cool" 2021-08-31 19:12:56,266 INFO SimpleSubprocess MakeCool - 0:01:26 2021-08-31 19:12:56,266 DEBUG SimpleSubprocess cp "/tmp/tmpip79d7tr/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-31 19:12:56,292 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:12:56,344 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt 2021-08-31 19:12:56,344 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-31 19:12:56,344 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 19:12:56,344 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 19:12:56,345 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-31 19:12:56,354 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/SRR5099910/__temp__/aligned/inter.pairs.txt" "/tmp/tmpfts5rzzn/inter_no_balanced.cool" 2021-08-31 19:14:17,886 INFO SimpleSubprocess MakeCool - 0:01:21 2021-08-31 19:14:17,886 DEBUG SimpleSubprocess cp "/tmp/tmpfts5rzzn/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-31 19:14:17,910 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:14:17,944 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt 2021-08-31 19:14:17,944 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-31 19:14:17,944 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 19:14:17,944 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 19:14:17,944 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-31 19:14:17,997 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/SRR5099910/__temp__/aligned/inter.pairs.txt" "/tmp/tmpmy4ats5p/inter_no_balanced.cool" 2021-08-31 19:15:36,604 INFO SimpleSubprocess MakeCool - 0:01:18 2021-08-31 19:15:36,604 DEBUG SimpleSubprocess cp "/tmp/tmpmy4ats5p/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-31 19:15:36,626 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:15:36,657 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt 2021-08-31 19:15:36,657 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-31 19:15:36,657 INFO Pairs2Cool Genome assembly: mm10 2021-08-31 19:15:36,657 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-31 19:15:36,658 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-31 19:15:36,687 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/SRR5099910/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2cyau6rh/inter_no_balanced.cool" 2021-08-31 19:16:52,912 INFO SimpleSubprocess MakeCool - 0:01:16 2021-08-31 19:16:52,912 DEBUG SimpleSubprocess cp "/tmp/tmp2cyau6rh/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-31 19:16:52,929 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:16:52,987 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-31 19:16:52,987 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_5kb.cool 2021-08-31 19:16:52,987 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 19:16:53,020 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpelnb__u2/inter.cool" 2021-08-31 19:16:53,050 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 19:16:53,050 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpelnb__u2/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 19:17:20,217 INFO SimpleSubprocess NormalizeCool - 0:00:27 2021-08-31 19:17:20,217 DEBUG SimpleSubprocess cp "/tmp/tmpelnb__u2/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_5kb.cool" 2021-08-31 19:17:20,249 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:17:20,276 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-31 19:17:20,276 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_10kb.cool 2021-08-31 19:17:20,276 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 19:17:20,323 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpzdutlwhb/inter.cool" 2021-08-31 19:17:20,350 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 19:17:20,350 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpzdutlwhb/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 19:17:35,872 INFO SimpleSubprocess NormalizeCool - 0:00:15 2021-08-31 19:17:35,872 DEBUG SimpleSubprocess cp "/tmp/tmpzdutlwhb/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_10kb.cool" 2021-08-31 19:17:35,898 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:17:35,926 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-31 19:17:35,926 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_20kb.cool 2021-08-31 19:17:35,926 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 19:17:35,930 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp68r9v87q/inter.cool" 2021-08-31 19:17:35,952 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 19:17:35,953 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp68r9v87q/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 19:17:47,222 INFO SimpleSubprocess NormalizeCool - 0:00:11 2021-08-31 19:17:47,246 DEBUG SimpleSubprocess cp "/tmp/tmp68r9v87q/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_20kb.cool" 2021-08-31 19:17:47,270 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:17:47,304 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-31 19:17:47,304 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_25kb.cool 2021-08-31 19:17:47,304 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 19:17:47,334 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpwy9vj92q/inter.cool" 2021-08-31 19:17:47,356 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 19:17:47,357 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpwy9vj92q/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 19:17:56,634 INFO SimpleSubprocess NormalizeCool - 0:00:09 2021-08-31 19:17:56,634 DEBUG SimpleSubprocess cp "/tmp/tmpwy9vj92q/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_25kb.cool" 2021-08-31 19:17:56,655 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:17:56,675 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-31 19:17:56,675 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_50kb.cool 2021-08-31 19:17:56,675 INFO CTaleNormalize Capture: chr1:70,945,000-81,010,000 2021-08-31 19:17:56,730 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpik73vq0n/inter.cool" 2021-08-31 19:17:56,748 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 19:17:56,748 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpik73vq0n/inter.cool" "chr1:70,945,000-81,010,000" 2021-08-31 19:18:01,340 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-08-31 19:18:01,340 DEBUG SimpleSubprocess cp "/tmp/tmpik73vq0n/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_50kb.cool" 2021-08-31 19:18:01,358 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:18:01,385 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt 2021-08-31 19:18:01,391 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-31 19:18:01,423 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_5kb.cool 2021-08-31 19:18:01,423 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt 2021-08-31 19:18:01,423 INFO AddWeight Chromosome: chr1 2021-08-31 19:18:01,423 INFO AddWeight Resolution [bp]: 5000 2021-08-31 19:18:06,029 INFO AddWeight AddWeight successfully finished 2021-08-31 19:18:06,030 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_10kb.cool 2021-08-31 19:18:06,030 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt 2021-08-31 19:18:06,030 INFO AddWeight Chromosome: chr1 2021-08-31 19:18:06,030 INFO AddWeight Resolution [bp]: 10000 2021-08-31 19:18:06,100 INFO AddWeight AddWeight successfully finished 2021-08-31 19:18:06,100 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_20kb.cool 2021-08-31 19:18:06,100 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt 2021-08-31 19:18:06,100 INFO AddWeight Chromosome: chr1 2021-08-31 19:18:06,100 INFO AddWeight Resolution [bp]: 20000 2021-08-31 19:18:06,142 INFO AddWeight AddWeight successfully finished 2021-08-31 19:18:06,142 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_25kb.cool 2021-08-31 19:18:06,142 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt 2021-08-31 19:18:06,142 INFO AddWeight Chromosome: chr1 2021-08-31 19:18:06,142 INFO AddWeight Resolution [bp]: 25000 2021-08-31 19:18:06,177 INFO AddWeight AddWeight successfully finished 2021-08-31 19:18:06,177 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_50kb.cool 2021-08-31 19:18:06,178 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt 2021-08-31 19:18:06,178 INFO AddWeight Chromosome: chr1 2021-08-31 19:18:06,178 INFO AddWeight Resolution [bp]: 50000 2021-08-31 19:18:06,203 INFO AddWeight AddWeight successfully finished 2021-08-31 19:18:06,206 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.hic 2021-08-31 19:18:06,206 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_norm.hic 2021-08-31 19:18:06,206 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt 2021-08-31 19:18:06,206 INFO Vector2HiC Threads: 10 2021-08-31 19:18:06,247 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.hic" "/tmp/tmpoxklc4ay/inter.hic" 2021-08-31 19:18:06,547 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-31 19:18:06,548 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-08-31 19:18:06,550 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpoxklc4ay/inter.hic" "/tmp/tmpoxklc4ay/vector.txt" 2021-08-31 19:18:11,347 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-31 19:18:11,347 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-08-31 19:18:11,349 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpoxklc4ay/inter.hic" "/tmp/tmpoxklc4ay/vector.txt" 2021-08-31 19:18:15,579 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-31 19:18:15,580 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-08-31 19:18:15,580 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpoxklc4ay/inter.hic" "/tmp/tmpoxklc4ay/vector.txt" 2021-08-31 19:18:19,474 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-31 19:18:19,475 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-08-31 19:18:19,475 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpoxklc4ay/inter.hic" "/tmp/tmpoxklc4ay/vector.txt" 2021-08-31 19:18:23,770 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-31 19:18:23,770 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-08-31 19:18:23,782 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpoxklc4ay/inter.hic" "/tmp/tmpoxklc4ay/vector.txt" 2021-08-31 19:18:27,995 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-31 19:18:27,995 DEBUG SimpleSubprocess cp "/tmp/tmpoxklc4ay/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_norm.hic" 2021-08-31 19:18:28,402 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-31 19:18:28,465 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/merged_nodups.txt" 2021-08-31 19:20:12,642 INFO SimpleSubprocess CopyResult - 0:01:44 2021-08-31 19:20:12,643 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter.pairs.txt" 2021-08-31 19:20:24,696 INFO SimpleSubprocess CopyResult - 0:00:12 2021-08-31 19:20:24,696 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/vector.txt" 2021-08-31 19:20:24,767 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:24,768 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter.hic" 2021-08-31 19:20:28,680 INFO SimpleSubprocess CopyResult - 0:00:03 2021-08-31 19:20:28,680 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_statistics.txt" 2021-08-31 19:20:28,716 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:28,717 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_no_balanced_5kb.cool" 2021-08-31 19:20:29,234 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:29,235 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_5kb.cool" 2021-08-31 19:20:29,695 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:29,696 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_no_balanced_10kb.cool" 2021-08-31 19:20:30,357 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:30,357 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_10kb.cool" 2021-08-31 19:20:30,543 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:30,543 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_no_balanced_20kb.cool" 2021-08-31 19:20:30,713 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:30,714 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_20kb.cool" 2021-08-31 19:20:31,421 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:31,422 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_no_balanced_25kb.cool" 2021-08-31 19:20:31,942 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:31,942 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_25kb.cool" 2021-08-31 19:20:32,219 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:32,219 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_no_balanced_50kb.cool" 2021-08-31 19:20:32,387 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:32,387 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/inter_50kb.cool" 2021-08-31 19:20:32,449 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-31 19:20:32,451 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__" 2021-08-31 19:21:00,167 INFO SimpleSubprocess RemoveTemp - 0:00:27 2021-08-31 19:21:00,201 INFO BenchmarkPipeline 'SRR5099910' FINISHED, SUMMARY TIME - 15:50:16 2021-09-01 12:23:13,448 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099910' --- 2021-09-01 12:23:13,470 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__" 2021-09-01 12:23:13,478 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,478 INFO BenchmarkPipeline 'SRR5099910' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,854 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099910' --- 2021-09-02 13:38:17,854 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099910/__temp__" 2021-09-02 13:38:17,861 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,861 INFO BenchmarkPipeline 'SRR5099910' FINISHED, SUMMARY TIME - 0:00:00