2021-09-03 15:58:57,011 INFO BenchmarkPipeline --- START PROCESSING 'SRR5855102-SRR5855103' --- 2021-09-03 15:58:57,011 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855102.sra 2021-09-03 15:58:57,011 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__ 2021-09-03 15:58:57,011 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpm2i6478e "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855102.sra" 2021-09-03 16:09:27,861 INFO SimpleSubprocess Sra2FastQ - 0:10:30 2021-09-03 16:09:27,861 DEBUG SimpleSubprocess gzip /tmp/tmpm2i6478e/* 2021-09-03 16:32:35,707 INFO SimpleSubprocess GZipFastQ - 0:23:07 2021-09-03 16:32:35,708 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/fastq"; mv /tmp/tmpm2i6478e/SRR5855102_2.fastq.gz /tmp/tmpm2i6478e/SRR5855102_R2.fastq.gz; mv /tmp/tmpm2i6478e/SRR5855102_1.fastq.gz /tmp/tmpm2i6478e/SRR5855102_R1.fastq.gz; cp /tmp/tmpm2i6478e/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/fastq" 2021-09-03 16:32:40,160 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-03 16:32:40,789 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855103.sra 2021-09-03 16:32:40,790 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__ 2021-09-03 16:32:40,790 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpdlulotwx "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855103.sra" 2021-09-03 16:43:29,306 INFO SimpleSubprocess Sra2FastQ - 0:10:48 2021-09-03 16:43:29,307 DEBUG SimpleSubprocess gzip /tmp/tmpdlulotwx/* 2021-09-03 17:06:20,680 INFO SimpleSubprocess GZipFastQ - 0:22:51 2021-09-03 17:06:20,680 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/fastq"; mv /tmp/tmpdlulotwx/SRR5855103_1.fastq.gz /tmp/tmpdlulotwx/SRR5855103_R1.fastq.gz; mv /tmp/tmpdlulotwx/SRR5855103_2.fastq.gz /tmp/tmpdlulotwx/SRR5855103_R2.fastq.gz; cp /tmp/tmpdlulotwx/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/fastq" 2021-09-03 17:06:24,986 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-03 17:06:25,573 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__ 2021-09-03 17:06:25,573 INFO Juicer Genome assembly: mm10 2021-09-03 17:06:25,573 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-03 17:06:25,573 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 17:06:25,573 INFO Juicer Enzyme: DpnII 2021-09-03 17:06:25,573 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-03 17:06:25,573 INFO Juicer Threads: 10 2021-09-03 17:06:25,573 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits" 2021-09-03 17:06:25,604 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-03 17:06:25,604 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/SRR5855102-SRR5855103/__temp__" 2021-09-04 00:00:19,280 INFO SimpleSubprocess Juicer - 6:53:53 2021-09-04 00:00:19,312 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/SRR5855102-SRR5855103/__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/SRR5855102-SRR5855103/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855102_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855102_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855102.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855102.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855103_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855103_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855103.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/splits/SRR5855103.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 [2021-09-03T21:26:00,775] [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 [2021-09-03T22:49:44,514] [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/SRR5855102-SRR5855103/__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 [2021-09-04T00:00:18,750] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__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/SRR5855102-SRR5855103/__temp__/aligned for results 2021-09-04 00:00:19,326 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/merged_nodups.txt 2021-09-04 00:00:19,326 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt 2021-09-04 00:00:19,327 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp8iqakt5f/inter.pairs.txt" 2021-09-04 00:01:59,243 INFO SimpleSubprocess MakeInterPairs - 0:01:39 2021-09-04 00:01:59,243 DEBUG SimpleSubprocess cp "/tmp/tmp8iqakt5f/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt" 2021-09-04 00:02:01,888 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-04 00:02:02,300 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt 2021-09-04 00:02:02,300 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-04 00:02:02,300 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 00:02:02,301 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 00:02:02,301 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-04 00:02:02,301 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/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt" "/tmp/tmpaq78pbhe/inter_no_balanced.cool" 2021-09-04 00:06:09,905 INFO SimpleSubprocess MakeCool - 0:04:07 2021-09-04 00:06:09,905 DEBUG SimpleSubprocess cp "/tmp/tmpaq78pbhe/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-04 00:06:10,050 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:06:10,069 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt 2021-09-04 00:06:10,069 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-04 00:06:10,069 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 00:06:10,070 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 00:06:10,070 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-04 00:06:10,070 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/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt" "/tmp/tmpttvrtmyv/inter_no_balanced.cool" 2021-09-04 00:09:59,189 INFO SimpleSubprocess MakeCool - 0:03:49 2021-09-04 00:09:59,189 DEBUG SimpleSubprocess cp "/tmp/tmpttvrtmyv/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-04 00:09:59,301 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:09:59,318 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt 2021-09-04 00:09:59,318 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-04 00:09:59,318 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 00:09:59,318 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 00:09:59,318 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-04 00:09:59,319 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/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt" "/tmp/tmp87lykige/inter_no_balanced.cool" 2021-09-04 00:13:33,024 INFO SimpleSubprocess MakeCool - 0:03:33 2021-09-04 00:13:33,024 DEBUG SimpleSubprocess cp "/tmp/tmp87lykige/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-04 00:13:33,121 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:13:33,135 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt 2021-09-04 00:13:33,135 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-04 00:13:33,135 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 00:13:33,135 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 00:13:33,135 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-04 00:13:33,136 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/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt" "/tmp/tmp16vm336d/inter_no_balanced.cool" 2021-09-04 00:16:58,230 INFO SimpleSubprocess MakeCool - 0:03:25 2021-09-04 00:16:58,230 DEBUG SimpleSubprocess cp "/tmp/tmp16vm336d/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-04 00:16:58,318 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:16:58,331 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt 2021-09-04 00:16:58,331 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-04 00:16:58,331 INFO Pairs2Cool Genome assembly: mm10 2021-09-04 00:16:58,331 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-04 00:16:58,331 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-04 00:16:58,331 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/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt" "/tmp/tmp8fkmrelf/inter_no_balanced.cool" 2021-09-04 00:20:09,335 INFO SimpleSubprocess MakeCool - 0:03:11 2021-09-04 00:20:09,335 DEBUG SimpleSubprocess cp "/tmp/tmp8fkmrelf/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-04 00:20:09,406 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:20:09,418 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-04 00:20:09,418 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_5kb.cool 2021-09-04 00:20:09,418 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 00:20:09,418 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmps0mjf8am/inter.cool" 2021-09-04 00:20:09,545 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 00:20:09,545 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmps0mjf8am/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 00:20:24,971 INFO SimpleSubprocess NormalizeCool - 0:00:15 2021-09-04 00:20:24,972 DEBUG SimpleSubprocess cp "/tmp/tmps0mjf8am/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_5kb.cool" 2021-09-04 00:20:25,100 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:20:25,121 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-04 00:20:25,121 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_10kb.cool 2021-09-04 00:20:25,121 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 00:20:25,121 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmptzn7f5t6/inter.cool" 2021-09-04 00:20:25,232 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 00:20:25,232 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmptzn7f5t6/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 00:20:43,753 INFO SimpleSubprocess NormalizeCool - 0:00:18 2021-09-04 00:20:43,753 DEBUG SimpleSubprocess cp "/tmp/tmptzn7f5t6/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_10kb.cool" 2021-09-04 00:20:43,864 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:20:43,879 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-04 00:20:43,879 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_20kb.cool 2021-09-04 00:20:43,879 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 00:20:43,880 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp1reqyw1a/inter.cool" 2021-09-04 00:20:43,976 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 00:20:43,976 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp1reqyw1a/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 00:20:58,535 INFO SimpleSubprocess NormalizeCool - 0:00:14 2021-09-04 00:20:58,535 DEBUG SimpleSubprocess cp "/tmp/tmp1reqyw1a/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_20kb.cool" 2021-09-04 00:20:58,630 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:20:58,644 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-04 00:20:58,644 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_25kb.cool 2021-09-04 00:20:58,644 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 00:20:58,645 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpiagvj3yz/inter.cool" 2021-09-04 00:20:58,730 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 00:20:58,731 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpiagvj3yz/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 00:21:12,908 INFO SimpleSubprocess NormalizeCool - 0:00:14 2021-09-04 00:21:12,909 DEBUG SimpleSubprocess cp "/tmp/tmpiagvj3yz/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_25kb.cool" 2021-09-04 00:21:13,025 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:21:13,038 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-04 00:21:13,038 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_50kb.cool 2021-09-04 00:21:13,038 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-04 00:21:13,039 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpuvb28o4f/inter.cool" 2021-09-04 00:21:13,116 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 00:21:13,117 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpuvb28o4f/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-04 00:21:23,154 INFO SimpleSubprocess NormalizeCool - 0:00:10 2021-09-04 00:21:23,154 DEBUG SimpleSubprocess cp "/tmp/tmpuvb28o4f/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_50kb.cool" 2021-09-04 00:21:23,230 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:21:23,244 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt 2021-09-04 00:21:23,252 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-04 00:21:23,252 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_5kb.cool 2021-09-04 00:21:23,252 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt 2021-09-04 00:21:23,252 INFO AddWeight Chromosome: chr2 2021-09-04 00:21:23,252 INFO AddWeight Resolution [bp]: 5000 2021-09-04 00:21:23,379 INFO AddWeight AddWeight successfully finished 2021-09-04 00:21:23,380 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_10kb.cool 2021-09-04 00:21:23,380 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt 2021-09-04 00:21:23,380 INFO AddWeight Chromosome: chr2 2021-09-04 00:21:23,380 INFO AddWeight Resolution [bp]: 10000 2021-09-04 00:21:23,430 INFO AddWeight AddWeight successfully finished 2021-09-04 00:21:23,430 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_20kb.cool 2021-09-04 00:21:23,430 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt 2021-09-04 00:21:23,430 INFO AddWeight Chromosome: chr2 2021-09-04 00:21:23,430 INFO AddWeight Resolution [bp]: 20000 2021-09-04 00:21:23,463 INFO AddWeight AddWeight successfully finished 2021-09-04 00:21:23,463 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_25kb.cool 2021-09-04 00:21:23,463 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt 2021-09-04 00:21:23,463 INFO AddWeight Chromosome: chr2 2021-09-04 00:21:23,463 INFO AddWeight Resolution [bp]: 25000 2021-09-04 00:21:23,492 INFO AddWeight AddWeight successfully finished 2021-09-04 00:21:23,492 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_50kb.cool 2021-09-04 00:21:23,492 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt 2021-09-04 00:21:23,492 INFO AddWeight Chromosome: chr2 2021-09-04 00:21:23,492 INFO AddWeight Resolution [bp]: 50000 2021-09-04 00:21:23,514 INFO AddWeight AddWeight successfully finished 2021-09-04 00:21:23,516 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.hic 2021-09-04 00:21:23,516 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_norm.hic 2021-09-04 00:21:23,516 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt 2021-09-04 00:21:23,516 INFO Vector2HiC Threads: 10 2021-09-04 00:21:23,547 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.hic" "/tmp/tmptq6pe8ta/inter.hic" 2021-09-04 00:21:24,464 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-04 00:21:24,464 INFO Vector2HiC Vector: vector c-tale_normalization chr2 5000 BP 2021-09-04 00:21:24,466 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmptq6pe8ta/inter.hic" "/tmp/tmptq6pe8ta/vector.txt" 2021-09-04 00:21:29,627 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-04 00:21:29,627 INFO Vector2HiC Vector: vector c-tale_normalization chr2 10000 BP 2021-09-04 00:21:29,628 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmptq6pe8ta/inter.hic" "/tmp/tmptq6pe8ta/vector.txt" 2021-09-04 00:21:33,913 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-04 00:21:33,913 INFO Vector2HiC Vector: vector c-tale_normalization chr2 20000 BP 2021-09-04 00:21:33,914 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmptq6pe8ta/inter.hic" "/tmp/tmptq6pe8ta/vector.txt" 2021-09-04 00:21:37,420 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-04 00:21:37,420 INFO Vector2HiC Vector: vector c-tale_normalization chr2 25000 BP 2021-09-04 00:21:37,420 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmptq6pe8ta/inter.hic" "/tmp/tmptq6pe8ta/vector.txt" 2021-09-04 00:21:41,446 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-04 00:21:41,446 INFO Vector2HiC Vector: vector c-tale_normalization chr2 50000 BP 2021-09-04 00:21:41,471 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmptq6pe8ta/inter.hic" "/tmp/tmptq6pe8ta/vector.txt" 2021-09-04 00:21:45,615 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-04 00:21:45,615 DEBUG SimpleSubprocess cp "/tmp/tmptq6pe8ta/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_norm.hic" 2021-09-04 00:21:46,568 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-04 00:21:47,316 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/merged_nodups.txt" 2021-09-04 00:23:29,188 INFO SimpleSubprocess CopyResult - 0:01:41 2021-09-04 00:23:29,212 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter.pairs.txt" 2021-09-04 00:23:51,264 INFO SimpleSubprocess CopyResult - 0:00:22 2021-09-04 00:23:51,265 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/vector.txt" 2021-09-04 00:23:51,405 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 00:23:51,405 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter.hic" 2021-09-04 00:24:02,991 INFO SimpleSubprocess CopyResult - 0:00:11 2021-09-04 00:24:02,991 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_statistics.txt" 2021-09-04 00:24:03,001 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 00:24:03,001 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_no_balanced_5kb.cool" 2021-09-04 00:24:05,823 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-04 00:24:05,823 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_5kb.cool" 2021-09-04 00:24:07,484 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 00:24:07,484 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_no_balanced_10kb.cool" 2021-09-04 00:24:09,213 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 00:24:09,214 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_10kb.cool" 2021-09-04 00:24:11,227 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-04 00:24:11,227 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_no_balanced_20kb.cool" 2021-09-04 00:24:12,946 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 00:24:12,946 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_20kb.cool" 2021-09-04 00:24:14,802 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 00:24:14,803 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_no_balanced_25kb.cool" 2021-09-04 00:24:16,226 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-04 00:24:16,226 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_25kb.cool" 2021-09-04 00:24:18,737 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-04 00:24:18,737 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_no_balanced_50kb.cool" 2021-09-04 00:24:19,432 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-04 00:24:19,432 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/inter_50kb.cool" 2021-09-04 00:24:21,438 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-04 00:24:21,647 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855102-SRR5855103/__temp__" 2021-09-04 00:24:27,603 INFO SimpleSubprocess RemoveTemp - 0:00:05 2021-09-04 00:24:27,603 INFO BenchmarkPipeline 'SRR5855102-SRR5855103' FINISHED, SUMMARY TIME - 8:25:30