2021-09-23 07:02:38,924 INFO BenchmarkPipeline --- START PROCESSING 'SRR7500319' --- 2021-09-23 07:02:38,925 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500319.sra 2021-09-23 07:02:38,925 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__ 2021-09-23 07:02:38,979 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmprot6puld "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500319.sra" 2021-09-23 07:21:54,355 INFO SimpleSubprocess Sra2FastQ - 0:19:15 2021-09-23 07:21:54,372 DEBUG SimpleSubprocess gzip /tmp/tmprot6puld/* 2021-09-23 08:14:51,603 INFO SimpleSubprocess GZipFastQ - 0:52:57 2021-09-23 08:14:51,603 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/fastq"; mv /tmp/tmprot6puld/SRR7500319_2.fastq.gz /tmp/tmprot6puld/SRR7500319_R2.fastq.gz; mv /tmp/tmprot6puld/SRR7500319_1.fastq.gz /tmp/tmprot6puld/SRR7500319_R1.fastq.gz; cp /tmp/tmprot6puld/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/fastq" 2021-09-23 08:15:22,045 INFO SimpleSubprocess CopyFiles - 0:00:30 2021-09-23 08:15:23,523 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__ 2021-09-23 08:15:23,524 INFO Juicer Genome assembly: mm10 2021-09-23 08:15:23,524 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-23 08:15:23,524 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 08:15:23,524 INFO Juicer Enzyme: DpnII 2021-09-23 08:15:23,524 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-23 08:15:23,524 INFO Juicer Threads: 10 2021-09-23 08:15:23,524 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/HIC_tmp" 2021-09-23 08:15:23,532 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-23 08:15:23,532 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/SRR7500319/__temp__" 2021-09-23 13:10:55,042 INFO SimpleSubprocess Juicer - 4:55:31 2021-09-23 13:10:55,074 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/SRR7500319/__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/SRR7500319/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/splits/SRR7500319_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/splits/SRR7500319_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/splits/SRR7500319.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/splits/SRR7500319.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 [2021-09-23T12:15:42,142] [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 [2021-09-23T12:38:21,236] [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/SRR7500319/__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 [2021-09-23T13:10:54,673] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__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/SRR7500319/__temp__/aligned for results 2021-09-23 13:10:55,140 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/merged_nodups.txt 2021-09-23 13:10:55,140 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt 2021-09-23 13:10:55,167 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpw7l5gb1z/inter.pairs.txt" 2021-09-23 13:11:41,925 INFO SimpleSubprocess MakeInterPairs - 0:00:46 2021-09-23 13:11:41,925 DEBUG SimpleSubprocess cp "/tmp/tmpw7l5gb1z/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt" 2021-09-23 13:11:43,063 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-23 13:11:43,232 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt 2021-09-23 13:11:43,232 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-23 13:11:43,232 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 13:11:43,232 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 13:11:43,232 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-23 13:11:43,249 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/SRR7500319/__temp__/aligned/inter.pairs.txt" "/tmp/tmp5vw88izk/inter_no_balanced.cool" 2021-09-23 13:12:55,907 INFO SimpleSubprocess MakeCool - 0:01:12 2021-09-23 13:12:55,907 DEBUG SimpleSubprocess cp "/tmp/tmp5vw88izk/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-23 13:12:55,935 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:12:55,939 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt 2021-09-23 13:12:55,939 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-23 13:12:55,939 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 13:12:55,939 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 13:12:55,939 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-23 13:12:55,964 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/SRR7500319/__temp__/aligned/inter.pairs.txt" "/tmp/tmpjm4kigk7/inter_no_balanced.cool" 2021-09-23 13:13:59,528 INFO SimpleSubprocess MakeCool - 0:01:03 2021-09-23 13:13:59,528 DEBUG SimpleSubprocess cp "/tmp/tmpjm4kigk7/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-23 13:13:59,550 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:13:59,553 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt 2021-09-23 13:13:59,553 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-23 13:13:59,553 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 13:13:59,553 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 13:13:59,553 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-23 13:13:59,570 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/SRR7500319/__temp__/aligned/inter.pairs.txt" "/tmp/tmp6g273nc4/inter_no_balanced.cool" 2021-09-23 13:14:59,747 INFO SimpleSubprocess MakeCool - 0:01:00 2021-09-23 13:14:59,747 DEBUG SimpleSubprocess cp "/tmp/tmp6g273nc4/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-23 13:14:59,768 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:14:59,770 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt 2021-09-23 13:14:59,770 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-23 13:14:59,770 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 13:14:59,770 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 13:14:59,771 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-23 13:14:59,810 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/SRR7500319/__temp__/aligned/inter.pairs.txt" "/tmp/tmpi76f96a7/inter_no_balanced.cool" 2021-09-23 13:15:56,889 INFO SimpleSubprocess MakeCool - 0:00:57 2021-09-23 13:15:56,889 DEBUG SimpleSubprocess cp "/tmp/tmpi76f96a7/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-23 13:15:56,908 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:15:56,910 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt 2021-09-23 13:15:56,911 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-23 13:15:56,911 INFO Pairs2Cool Genome assembly: mm10 2021-09-23 13:15:56,911 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-23 13:15:56,911 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-23 13:15:56,911 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/SRR7500319/__temp__/aligned/inter.pairs.txt" "/tmp/tmpwpusjh58/inter_no_balanced.cool" 2021-09-23 13:16:52,473 INFO SimpleSubprocess MakeCool - 0:00:55 2021-09-23 13:16:52,473 DEBUG SimpleSubprocess cp "/tmp/tmpwpusjh58/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-23 13:16:52,489 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:16:52,493 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-23 13:16:52,493 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_5kb.cool 2021-09-23 13:16:52,493 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 13:16:52,514 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmplh7e2qth/inter.cool" 2021-09-23 13:16:52,541 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 13:16:52,541 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmplh7e2qth/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 13:17:14,760 INFO SimpleSubprocess NormalizeCool - 0:00:22 2021-09-23 13:17:14,760 DEBUG SimpleSubprocess cp "/tmp/tmplh7e2qth/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_5kb.cool" 2021-09-23 13:17:14,788 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:17:14,791 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-23 13:17:14,792 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_10kb.cool 2021-09-23 13:17:14,792 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 13:17:14,792 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpsik46wk9/inter.cool" 2021-09-23 13:17:14,816 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 13:17:14,816 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpsik46wk9/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 13:17:18,904 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-23 13:17:18,904 DEBUG SimpleSubprocess cp "/tmp/tmpsik46wk9/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_10kb.cool" 2021-09-23 13:17:18,928 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:17:18,931 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-23 13:17:18,931 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_20kb.cool 2021-09-23 13:17:18,931 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 13:17:18,952 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpfp3j07y6/inter.cool" 2021-09-23 13:17:18,972 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 13:17:18,973 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpfp3j07y6/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 13:17:22,050 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-23 13:17:22,051 DEBUG SimpleSubprocess cp "/tmp/tmpfp3j07y6/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_20kb.cool" 2021-09-23 13:17:22,071 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:17:22,074 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-23 13:17:22,074 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_25kb.cool 2021-09-23 13:17:22,074 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 13:17:22,074 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp5ndwn1ps/inter.cool" 2021-09-23 13:17:22,094 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 13:17:22,094 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp5ndwn1ps/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 13:17:24,939 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-23 13:17:24,939 DEBUG SimpleSubprocess cp "/tmp/tmp5ndwn1ps/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_25kb.cool" 2021-09-23 13:17:24,959 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:17:24,961 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-23 13:17:24,961 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_50kb.cool 2021-09-23 13:17:24,961 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-23 13:17:24,981 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpq90lnp2e/inter.cool" 2021-09-23 13:17:24,998 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 13:17:24,998 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpq90lnp2e/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-23 13:17:26,848 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-23 13:17:26,848 DEBUG SimpleSubprocess cp "/tmp/tmpq90lnp2e/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_50kb.cool" 2021-09-23 13:17:26,866 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:17:26,870 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt 2021-09-23 13:17:26,876 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-23 13:17:26,876 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_5kb.cool 2021-09-23 13:17:26,877 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt 2021-09-23 13:17:26,877 INFO AddWeight Chromosome: chr1 2021-09-23 13:17:26,877 INFO AddWeight Resolution [bp]: 5000 2021-09-23 13:17:26,973 INFO AddWeight AddWeight successfully finished 2021-09-23 13:17:26,973 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_10kb.cool 2021-09-23 13:17:26,974 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt 2021-09-23 13:17:26,974 INFO AddWeight Chromosome: chr1 2021-09-23 13:17:26,974 INFO AddWeight Resolution [bp]: 10000 2021-09-23 13:17:27,050 INFO AddWeight AddWeight successfully finished 2021-09-23 13:17:27,050 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_20kb.cool 2021-09-23 13:17:27,063 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt 2021-09-23 13:17:27,063 INFO AddWeight Chromosome: chr1 2021-09-23 13:17:27,063 INFO AddWeight Resolution [bp]: 20000 2021-09-23 13:17:27,109 INFO AddWeight AddWeight successfully finished 2021-09-23 13:17:27,109 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_25kb.cool 2021-09-23 13:17:27,109 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt 2021-09-23 13:17:27,109 INFO AddWeight Chromosome: chr1 2021-09-23 13:17:27,109 INFO AddWeight Resolution [bp]: 25000 2021-09-23 13:17:27,148 INFO AddWeight AddWeight successfully finished 2021-09-23 13:17:27,149 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_50kb.cool 2021-09-23 13:17:27,149 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt 2021-09-23 13:17:27,149 INFO AddWeight Chromosome: chr1 2021-09-23 13:17:27,149 INFO AddWeight Resolution [bp]: 50000 2021-09-23 13:17:27,176 INFO AddWeight AddWeight successfully finished 2021-09-23 13:17:27,178 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.hic 2021-09-23 13:17:27,178 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_norm.hic 2021-09-23 13:17:27,178 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt 2021-09-23 13:17:27,178 INFO Vector2HiC Threads: 10 2021-09-23 13:17:27,336 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.hic" "/tmp/tmpjfozo_en/inter.hic" 2021-09-23 13:17:27,594 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-23 13:17:27,594 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-09-23 13:17:27,595 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpjfozo_en/inter.hic" "/tmp/tmpjfozo_en/vector.txt" 2021-09-23 13:17:32,381 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-23 13:17:32,381 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-09-23 13:17:32,382 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpjfozo_en/inter.hic" "/tmp/tmpjfozo_en/vector.txt" 2021-09-23 13:17:36,577 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-23 13:17:36,578 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-09-23 13:17:36,579 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpjfozo_en/inter.hic" "/tmp/tmpjfozo_en/vector.txt" 2021-09-23 13:17:40,286 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 13:17:40,287 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-09-23 13:17:40,287 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpjfozo_en/inter.hic" "/tmp/tmpjfozo_en/vector.txt" 2021-09-23 13:17:44,196 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-23 13:17:44,196 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-09-23 13:17:44,197 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpjfozo_en/inter.hic" "/tmp/tmpjfozo_en/vector.txt" 2021-09-23 13:17:48,299 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-23 13:17:48,300 DEBUG SimpleSubprocess cp "/tmp/tmpjfozo_en/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_norm.hic" 2021-09-23 13:17:48,610 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-23 13:17:48,787 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/merged_nodups.txt" 2021-09-23 13:18:03,240 INFO SimpleSubprocess CopyResult - 0:00:14 2021-09-23 13:18:03,240 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter.pairs.txt" 2021-09-23 13:18:14,366 INFO SimpleSubprocess CopyResult - 0:00:11 2021-09-23 13:18:14,367 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/vector.txt" 2021-09-23 13:18:14,376 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:14,377 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter.hic" 2021-09-23 13:18:17,319 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-23 13:18:17,319 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_statistics.txt" 2021-09-23 13:18:17,327 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:17,327 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_no_balanced_5kb.cool" 2021-09-23 13:18:17,476 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:17,477 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_5kb.cool" 2021-09-23 13:18:17,604 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:17,604 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_no_balanced_10kb.cool" 2021-09-23 13:18:17,739 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:17,739 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_10kb.cool" 2021-09-23 13:18:17,871 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:17,872 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_no_balanced_20kb.cool" 2021-09-23 13:18:17,975 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:17,976 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_20kb.cool" 2021-09-23 13:18:18,091 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:18,092 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_no_balanced_25kb.cool" 2021-09-23 13:18:18,200 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:18,200 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_25kb.cool" 2021-09-23 13:18:18,288 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:18,288 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_no_balanced_50kb.cool" 2021-09-23 13:18:18,371 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:18,371 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/inter_50kb.cool" 2021-09-23 13:18:18,455 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-23 13:18:18,503 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500319/__temp__" 2021-09-23 13:18:26,107 INFO SimpleSubprocess RemoveTemp - 0:00:07 2021-09-23 13:18:26,107 INFO BenchmarkPipeline 'SRR7500319' FINISHED, SUMMARY TIME - 6:15:47