2021-08-28 21:01:53,002 INFO BenchmarkPipeline --- START PROCESSING 'SRR3733921' --- 2021-08-28 21:01:53,003 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3733921.sra 2021-08-28 21:01:53,003 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__ 2021-08-28 21:01:53,003 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpdiguij1y "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3733921.sra" 2021-08-28 21:24:52,564 INFO SimpleSubprocess Sra2FastQ - 0:22:59 2021-08-28 21:24:52,574 DEBUG SimpleSubprocess gzip /tmp/tmpdiguij1y/* 2021-08-28 22:39:58,677 INFO SimpleSubprocess GZipFastQ - 1:15:06 2021-08-28 22:39:58,744 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/fastq"; mv /tmp/tmpdiguij1y/SRR3733921_1.fastq.gz /tmp/tmpdiguij1y/SRR3733921_R1.fastq.gz; mv /tmp/tmpdiguij1y/SRR3733921_2.fastq.gz /tmp/tmpdiguij1y/SRR3733921_R2.fastq.gz; cp /tmp/tmpdiguij1y/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/fastq" 2021-08-28 22:40:49,648 INFO SimpleSubprocess CopyFiles - 0:00:50 2021-08-28 22:40:51,015 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__ 2021-08-28 22:40:51,015 INFO Juicer Genome assembly: mm10 2021-08-28 22:40:51,015 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-28 22:40:51,015 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 22:40:51,015 INFO Juicer Enzyme: DpnII 2021-08-28 22:40:51,015 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-28 22:40:51,015 INFO Juicer Threads: 10 2021-08-28 22:40:51,015 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/SRR3733921/__temp__" 2021-08-29 03:59:20,189 INFO SimpleSubprocess Juicer - 5:18:29 2021-08-29 03:59:20,203 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/SRR3733921/__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/SRR3733921/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/splits/SRR3733921_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/splits/SRR3733921_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/splits/SRR3733921.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/splits/SRR3733921.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 [2021-08-29T03:24:18,750] [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 [2021-08-29T03:44:36,671] [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/SRR3733921/__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 [2021-08-29T03:59:19,758] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__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/SRR3733921/__temp__/aligned for results 2021-08-29 03:59:20,269 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/merged_nodups.txt 2021-08-29 03:59:20,269 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt 2021-08-29 03:59:20,270 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp8ysis354/inter.pairs.txt" 2021-08-29 03:59:58,431 INFO SimpleSubprocess MakeInterPairs - 0:00:38 2021-08-29 03:59:58,431 DEBUG SimpleSubprocess cp "/tmp/tmp8ysis354/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt" 2021-08-29 03:59:59,473 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-29 04:00:00,241 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt 2021-08-29 04:00:00,241 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 04:00:00,241 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 04:00:00,241 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 04:00:00,241 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-29 04:00:00,242 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/SRR3733921/__temp__/aligned/inter.pairs.txt" "/tmp/tmpxc6l92s8/inter_no_balanced.cool" 2021-08-29 04:01:02,561 INFO SimpleSubprocess MakeCool - 0:01:02 2021-08-29 04:01:02,562 DEBUG SimpleSubprocess cp "/tmp/tmpxc6l92s8/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-29 04:01:02,589 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:01:02,592 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt 2021-08-29 04:01:02,592 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 04:01:02,592 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 04:01:02,592 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 04:01:02,592 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-29 04:01:02,592 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/SRR3733921/__temp__/aligned/inter.pairs.txt" "/tmp/tmppb0__m7w/inter_no_balanced.cool" 2021-08-29 04:01:54,435 INFO SimpleSubprocess MakeCool - 0:00:51 2021-08-29 04:01:54,435 DEBUG SimpleSubprocess cp "/tmp/tmppb0__m7w/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-29 04:01:54,454 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:01:54,482 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt 2021-08-29 04:01:54,482 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 04:01:54,482 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 04:01:54,483 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 04:01:54,483 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-29 04:01:54,483 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/SRR3733921/__temp__/aligned/inter.pairs.txt" "/tmp/tmpkmz_j0wg/inter_no_balanced.cool" 2021-08-29 04:02:44,295 INFO SimpleSubprocess MakeCool - 0:00:49 2021-08-29 04:02:44,295 DEBUG SimpleSubprocess cp "/tmp/tmpkmz_j0wg/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-29 04:02:44,312 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:02:44,314 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt 2021-08-29 04:02:44,314 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 04:02:44,314 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 04:02:44,314 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 04:02:44,314 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-29 04:02:44,345 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/SRR3733921/__temp__/aligned/inter.pairs.txt" "/tmp/tmpts32ww2g/inter_no_balanced.cool" 2021-08-29 04:03:34,116 INFO SimpleSubprocess MakeCool - 0:00:49 2021-08-29 04:03:34,116 DEBUG SimpleSubprocess cp "/tmp/tmpts32ww2g/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-29 04:03:34,131 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:03:34,133 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt 2021-08-29 04:03:34,133 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 04:03:34,133 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 04:03:34,133 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 04:03:34,133 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-29 04:03:34,133 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/SRR3733921/__temp__/aligned/inter.pairs.txt" "/tmp/tmpexjxgxr_/inter_no_balanced.cool" 2021-08-29 04:04:22,259 INFO SimpleSubprocess MakeCool - 0:00:48 2021-08-29 04:04:22,260 DEBUG SimpleSubprocess cp "/tmp/tmpexjxgxr_/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-29 04:04:22,273 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:04:22,276 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 04:04:22,276 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_5kb.cool 2021-08-29 04:04:22,276 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 04:04:22,277 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpggnhwvbl/inter.cool" 2021-08-29 04:04:22,297 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 04:04:22,297 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpggnhwvbl/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 04:04:27,052 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-08-29 04:04:27,052 DEBUG SimpleSubprocess cp "/tmp/tmpggnhwvbl/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_5kb.cool" 2021-08-29 04:04:27,075 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:04:27,077 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 04:04:27,078 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_10kb.cool 2021-08-29 04:04:27,078 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 04:04:27,078 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpu4mp00c7/inter.cool" 2021-08-29 04:04:27,097 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 04:04:27,097 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpu4mp00c7/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 04:04:29,437 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-29 04:04:29,438 DEBUG SimpleSubprocess cp "/tmp/tmpu4mp00c7/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_10kb.cool" 2021-08-29 04:04:29,456 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:04:29,487 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 04:04:29,487 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_20kb.cool 2021-08-29 04:04:29,487 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 04:04:29,487 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpjteg0md8/inter.cool" 2021-08-29 04:04:29,503 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 04:04:29,503 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpjteg0md8/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 04:04:31,181 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 04:04:31,181 DEBUG SimpleSubprocess cp "/tmp/tmpjteg0md8/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_20kb.cool" 2021-08-29 04:04:31,197 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:04:31,199 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 04:04:31,199 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_25kb.cool 2021-08-29 04:04:31,199 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 04:04:31,199 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpz3k2cfcq/inter.cool" 2021-08-29 04:04:31,214 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 04:04:31,214 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpz3k2cfcq/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 04:04:32,796 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 04:04:32,796 DEBUG SimpleSubprocess cp "/tmp/tmpz3k2cfcq/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_25kb.cool" 2021-08-29 04:04:32,811 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:04:32,813 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 04:04:32,813 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_50kb.cool 2021-08-29 04:04:32,813 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 04:04:32,830 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp_1gomgyd/inter.cool" 2021-08-29 04:04:32,843 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 04:04:32,843 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp_1gomgyd/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 04:04:34,038 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 04:04:34,038 DEBUG SimpleSubprocess cp "/tmp/tmp_1gomgyd/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_50kb.cool" 2021-08-29 04:04:34,053 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:04:34,056 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt 2021-08-29 04:04:34,062 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-29 04:04:34,062 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_5kb.cool 2021-08-29 04:04:34,062 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt 2021-08-29 04:04:34,062 INFO AddWeight Chromosome: chr11 2021-08-29 04:04:34,062 INFO AddWeight Resolution [bp]: 5000 2021-08-29 04:04:34,147 INFO AddWeight AddWeight successfully finished 2021-08-29 04:04:34,147 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_10kb.cool 2021-08-29 04:04:34,147 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt 2021-08-29 04:04:34,147 INFO AddWeight Chromosome: chr11 2021-08-29 04:04:34,147 INFO AddWeight Resolution [bp]: 10000 2021-08-29 04:04:34,195 INFO AddWeight AddWeight successfully finished 2021-08-29 04:04:34,195 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_20kb.cool 2021-08-29 04:04:34,195 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt 2021-08-29 04:04:34,195 INFO AddWeight Chromosome: chr11 2021-08-29 04:04:34,195 INFO AddWeight Resolution [bp]: 20000 2021-08-29 04:04:34,226 INFO AddWeight AddWeight successfully finished 2021-08-29 04:04:34,226 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_25kb.cool 2021-08-29 04:04:34,226 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt 2021-08-29 04:04:34,226 INFO AddWeight Chromosome: chr11 2021-08-29 04:04:34,226 INFO AddWeight Resolution [bp]: 25000 2021-08-29 04:04:34,254 INFO AddWeight AddWeight successfully finished 2021-08-29 04:04:34,254 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_50kb.cool 2021-08-29 04:04:34,254 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt 2021-08-29 04:04:34,254 INFO AddWeight Chromosome: chr11 2021-08-29 04:04:34,254 INFO AddWeight Resolution [bp]: 50000 2021-08-29 04:04:34,275 INFO AddWeight AddWeight successfully finished 2021-08-29 04:04:34,277 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.hic 2021-08-29 04:04:34,277 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_norm.hic 2021-08-29 04:04:34,277 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt 2021-08-29 04:04:34,277 INFO Vector2HiC Threads: 10 2021-08-29 04:04:34,312 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.hic" "/tmp/tmpnmy9sljd/inter.hic" 2021-08-29 04:04:34,573 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 04:04:34,573 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-08-29 04:04:34,576 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpnmy9sljd/inter.hic" "/tmp/tmpnmy9sljd/vector.txt" 2021-08-29 04:04:39,080 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 04:04:39,081 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-08-29 04:04:39,082 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpnmy9sljd/inter.hic" "/tmp/tmpnmy9sljd/vector.txt" 2021-08-29 04:04:42,914 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 04:04:42,914 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-08-29 04:04:42,915 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpnmy9sljd/inter.hic" "/tmp/tmpnmy9sljd/vector.txt" 2021-08-29 04:04:46,620 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 04:04:46,621 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-08-29 04:04:46,621 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpnmy9sljd/inter.hic" "/tmp/tmpnmy9sljd/vector.txt" 2021-08-29 04:04:50,312 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 04:04:50,312 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-08-29 04:04:50,313 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpnmy9sljd/inter.hic" "/tmp/tmpnmy9sljd/vector.txt" 2021-08-29 04:04:54,089 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 04:04:54,089 DEBUG SimpleSubprocess cp "/tmp/tmpnmy9sljd/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_norm.hic" 2021-08-29 04:04:54,385 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 04:04:54,433 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/merged_nodups.txt" 2021-08-29 04:05:10,563 INFO SimpleSubprocess CopyResult - 0:00:16 2021-08-29 04:05:10,564 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter.pairs.txt" 2021-08-29 04:05:16,499 INFO SimpleSubprocess CopyResult - 0:00:05 2021-08-29 04:05:16,499 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/vector.txt" 2021-08-29 04:05:16,507 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:16,507 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter.hic" 2021-08-29 04:05:18,667 INFO SimpleSubprocess CopyResult - 0:00:02 2021-08-29 04:05:18,668 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_statistics.txt" 2021-08-29 04:05:18,820 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:18,820 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_no_balanced_5kb.cool" 2021-08-29 04:05:18,922 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:18,923 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_5kb.cool" 2021-08-29 04:05:19,003 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,003 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_no_balanced_10kb.cool" 2021-08-29 04:05:19,060 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,060 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_10kb.cool" 2021-08-29 04:05:19,116 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,116 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_no_balanced_20kb.cool" 2021-08-29 04:05:19,161 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,161 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_20kb.cool" 2021-08-29 04:05:19,204 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,204 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_no_balanced_25kb.cool" 2021-08-29 04:05:19,248 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,248 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_25kb.cool" 2021-08-29 04:05:19,292 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,292 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_no_balanced_50kb.cool" 2021-08-29 04:05:19,324 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,324 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/inter_50kb.cool" 2021-08-29 04:05:19,366 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 04:05:19,557 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__" 2021-08-29 04:05:26,545 INFO SimpleSubprocess RemoveTemp - 0:00:06 2021-08-29 04:05:26,545 INFO BenchmarkPipeline 'SRR3733921' FINISHED, SUMMARY TIME - 7:03:33 2021-09-01 12:23:13,346 INFO BenchmarkPipeline --- START PROCESSING 'SRR3733921' --- 2021-09-01 12:23:13,347 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__" 2021-09-01 12:23:13,356 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,356 INFO BenchmarkPipeline 'SRR3733921' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,805 INFO BenchmarkPipeline --- START PROCESSING 'SRR3733921' --- 2021-09-02 13:38:17,805 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733921/__temp__" 2021-09-02 13:38:17,810 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,810 INFO BenchmarkPipeline 'SRR3733921' FINISHED, SUMMARY TIME - 0:00:00