2021-09-25 03:09:14,236 INFO BenchmarkPipeline --- START PROCESSING 'SRR8284499-SRR8984910' --- 2021-09-25 03:09:14,236 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284499.sra 2021-09-25 03:09:14,236 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__ 2021-09-25 03:09:14,237 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpcxtouwt9 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284499.sra" 2021-09-25 03:30:31,196 INFO SimpleSubprocess Sra2FastQ - 0:21:16 2021-09-25 03:30:31,212 DEBUG SimpleSubprocess gzip /tmp/tmpcxtouwt9/* 2021-09-25 04:33:52,773 INFO SimpleSubprocess GZipFastQ - 1:03:21 2021-09-25 04:33:52,891 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/fastq"; mv /tmp/tmpcxtouwt9/SRR8284499_2.fastq.gz /tmp/tmpcxtouwt9/SRR8284499_R2.fastq.gz; mv /tmp/tmpcxtouwt9/SRR8284499_1.fastq.gz /tmp/tmpcxtouwt9/SRR8284499_R1.fastq.gz; cp /tmp/tmpcxtouwt9/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/fastq" 2021-09-25 04:34:28,274 INFO SimpleSubprocess CopyFiles - 0:00:35 2021-09-25 04:34:29,866 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984910.sra 2021-09-25 04:34:29,866 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__ 2021-09-25 04:34:29,866 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp8bm5s63y "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984910.sra" 2021-09-25 04:58:15,292 INFO SimpleSubprocess Sra2FastQ - 0:23:45 2021-09-25 04:58:15,312 DEBUG SimpleSubprocess gzip /tmp/tmp8bm5s63y/* 2021-09-25 06:08:16,825 INFO SimpleSubprocess GZipFastQ - 1:10:01 2021-09-25 06:08:16,887 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/fastq"; mv /tmp/tmp8bm5s63y/SRR8984910_1.fastq.gz /tmp/tmp8bm5s63y/SRR8984910_R1.fastq.gz; mv /tmp/tmp8bm5s63y/SRR8984910_2.fastq.gz /tmp/tmp8bm5s63y/SRR8984910_R2.fastq.gz; cp /tmp/tmp8bm5s63y/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/fastq" 2021-09-25 06:09:07,695 INFO SimpleSubprocess CopyFiles - 0:00:50 2021-09-25 06:09:09,597 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__ 2021-09-25 06:09:09,597 INFO Juicer Genome assembly: mm10 2021-09-25 06:09:09,597 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-25 06:09:09,597 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 06:09:09,597 INFO Juicer Enzyme: DpnII 2021-09-25 06:09:09,597 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-25 06:09:09,597 INFO Juicer Threads: 10 2021-09-25 06:09:09,597 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/HIC_tmp" 2021-09-25 06:09:09,778 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-25 06:09:09,778 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/SRR8284499-SRR8984910/__temp__" 2021-09-25 18:21:14,894 INFO SimpleSubprocess Juicer - 12:12:05 2021-09-25 18:21:14,933 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/SRR8284499-SRR8984910/__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/SRR8284499-SRR8984910/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8284499_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8284499_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8284499.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8284499.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8984910_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8984910_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8984910.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/splits/SRR8984910.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 [2021-09-25T16:25:29,465] [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 [2021-09-25T17:16:58,015] [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/SRR8284499-SRR8984910/__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 [2021-09-25T18:21:14,461] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__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/SRR8284499-SRR8984910/__temp__/aligned for results 2021-09-25 18:21:15,018 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/merged_nodups.txt 2021-09-25 18:21:15,019 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt 2021-09-25 18:21:15,058 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpv_v3d9lx/inter.pairs.txt" 2021-09-25 18:22:38,835 INFO SimpleSubprocess MakeInterPairs - 0:01:23 2021-09-25 18:22:38,835 DEBUG SimpleSubprocess cp "/tmp/tmpv_v3d9lx/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt" 2021-09-25 18:22:40,942 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-25 18:22:41,265 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt 2021-09-25 18:22:41,266 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-25 18:22:41,266 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 18:22:41,266 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 18:22:41,266 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-25 18:22:41,266 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/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt" "/tmp/tmpd9_7xw6j/inter_no_balanced.cool" 2021-09-25 18:25:04,857 INFO SimpleSubprocess MakeCool - 0:02:23 2021-09-25 18:25:04,857 DEBUG SimpleSubprocess cp "/tmp/tmpd9_7xw6j/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-25 18:25:04,914 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:25:04,920 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt 2021-09-25 18:25:04,920 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-25 18:25:04,920 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 18:25:04,920 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 18:25:04,920 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-25 18:25:04,921 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/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt" "/tmp/tmpanabvbse/inter_no_balanced.cool" 2021-09-25 18:27:03,740 INFO SimpleSubprocess MakeCool - 0:01:58 2021-09-25 18:27:03,740 DEBUG SimpleSubprocess cp "/tmp/tmpanabvbse/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-25 18:27:03,779 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:27:03,784 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt 2021-09-25 18:27:03,784 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-25 18:27:03,784 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 18:27:03,784 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 18:27:03,784 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-25 18:27:03,811 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/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt" "/tmp/tmp22eyi0bv/inter_no_balanced.cool" 2021-09-25 18:28:57,542 INFO SimpleSubprocess MakeCool - 0:01:53 2021-09-25 18:28:57,542 DEBUG SimpleSubprocess cp "/tmp/tmp22eyi0bv/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-25 18:28:57,576 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:28:57,608 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt 2021-09-25 18:28:57,609 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-25 18:28:57,609 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 18:28:57,609 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 18:28:57,609 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-25 18:28:57,609 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/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt" "/tmp/tmppksvbhym/inter_no_balanced.cool" 2021-09-25 18:30:45,951 INFO SimpleSubprocess MakeCool - 0:01:48 2021-09-25 18:30:45,951 DEBUG SimpleSubprocess cp "/tmp/tmppksvbhym/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-25 18:30:45,984 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:30:45,988 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt 2021-09-25 18:30:45,988 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-25 18:30:45,988 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 18:30:45,988 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 18:30:45,988 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-25 18:30:45,989 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/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt" "/tmp/tmpiuwob34n/inter_no_balanced.cool" 2021-09-25 18:32:29,619 INFO SimpleSubprocess MakeCool - 0:01:43 2021-09-25 18:32:29,619 DEBUG SimpleSubprocess cp "/tmp/tmpiuwob34n/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-25 18:32:29,645 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:32:29,709 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-25 18:32:29,709 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_5kb.cool 2021-09-25 18:32:29,709 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 18:32:29,709 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpln1et42x/inter.cool" 2021-09-25 18:32:29,758 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 18:32:29,758 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpln1et42x/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 18:32:51,278 INFO SimpleSubprocess NormalizeCool - 0:00:21 2021-09-25 18:32:51,279 DEBUG SimpleSubprocess cp "/tmp/tmpln1et42x/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_5kb.cool" 2021-09-25 18:32:51,328 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:32:51,334 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-25 18:32:51,334 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_10kb.cool 2021-09-25 18:32:51,334 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 18:32:51,363 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpubfqpf0k/inter.cool" 2021-09-25 18:32:51,405 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 18:32:51,405 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpubfqpf0k/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 18:33:06,243 INFO SimpleSubprocess NormalizeCool - 0:00:14 2021-09-25 18:33:06,244 DEBUG SimpleSubprocess cp "/tmp/tmpubfqpf0k/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_10kb.cool" 2021-09-25 18:33:06,283 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:33:06,287 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-25 18:33:06,287 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_20kb.cool 2021-09-25 18:33:06,287 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 18:33:06,288 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp6i3zfhuh/inter.cool" 2021-09-25 18:33:06,321 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 18:33:06,322 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp6i3zfhuh/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 18:33:15,398 INFO SimpleSubprocess NormalizeCool - 0:00:09 2021-09-25 18:33:15,399 DEBUG SimpleSubprocess cp "/tmp/tmp6i3zfhuh/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_20kb.cool" 2021-09-25 18:33:15,435 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:33:15,440 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-25 18:33:15,440 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_25kb.cool 2021-09-25 18:33:15,440 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 18:33:15,440 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpglgm9ekv/inter.cool" 2021-09-25 18:33:15,474 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 18:33:15,474 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpglgm9ekv/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 18:33:23,166 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-25 18:33:23,166 DEBUG SimpleSubprocess cp "/tmp/tmpglgm9ekv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_25kb.cool" 2021-09-25 18:33:23,199 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:33:23,230 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-25 18:33:23,230 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_50kb.cool 2021-09-25 18:33:23,230 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 18:33:23,230 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp6hduudpk/inter.cool" 2021-09-25 18:33:23,260 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 18:33:23,261 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp6hduudpk/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 18:33:27,457 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-25 18:33:27,457 DEBUG SimpleSubprocess cp "/tmp/tmp6hduudpk/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_50kb.cool" 2021-09-25 18:33:27,485 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:33:27,490 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt 2021-09-25 18:33:27,505 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-25 18:33:27,533 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_5kb.cool 2021-09-25 18:33:27,534 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt 2021-09-25 18:33:27,534 INFO AddWeight Chromosome: chr5 2021-09-25 18:33:27,534 INFO AddWeight Resolution [bp]: 5000 2021-09-25 18:33:28,282 INFO AddWeight AddWeight successfully finished 2021-09-25 18:33:28,283 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_10kb.cool 2021-09-25 18:33:28,283 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt 2021-09-25 18:33:28,283 INFO AddWeight Chromosome: chr5 2021-09-25 18:33:28,283 INFO AddWeight Resolution [bp]: 10000 2021-09-25 18:33:28,324 INFO AddWeight AddWeight successfully finished 2021-09-25 18:33:28,324 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_20kb.cool 2021-09-25 18:33:28,324 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt 2021-09-25 18:33:28,324 INFO AddWeight Chromosome: chr5 2021-09-25 18:33:28,324 INFO AddWeight Resolution [bp]: 20000 2021-09-25 18:33:28,353 INFO AddWeight AddWeight successfully finished 2021-09-25 18:33:28,353 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_25kb.cool 2021-09-25 18:33:28,353 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt 2021-09-25 18:33:28,353 INFO AddWeight Chromosome: chr5 2021-09-25 18:33:28,353 INFO AddWeight Resolution [bp]: 25000 2021-09-25 18:33:28,377 INFO AddWeight AddWeight successfully finished 2021-09-25 18:33:28,378 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_50kb.cool 2021-09-25 18:33:28,378 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt 2021-09-25 18:33:28,378 INFO AddWeight Chromosome: chr5 2021-09-25 18:33:28,378 INFO AddWeight Resolution [bp]: 50000 2021-09-25 18:33:28,397 INFO AddWeight AddWeight successfully finished 2021-09-25 18:33:28,399 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.hic 2021-09-25 18:33:28,399 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_norm.hic 2021-09-25 18:33:28,399 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt 2021-09-25 18:33:28,399 INFO Vector2HiC Threads: 10 2021-09-25 18:33:28,422 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.hic" "/tmp/tmpv2x4kjqw/inter.hic" 2021-09-25 18:33:29,321 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 18:33:29,321 INFO Vector2HiC Vector: vector c-tale_normalization chr5 5000 BP 2021-09-25 18:33:29,322 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpv2x4kjqw/inter.hic" "/tmp/tmpv2x4kjqw/vector.txt" 2021-09-25 18:33:34,345 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-25 18:33:34,345 INFO Vector2HiC Vector: vector c-tale_normalization chr5 10000 BP 2021-09-25 18:33:34,346 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpv2x4kjqw/inter.hic" "/tmp/tmpv2x4kjqw/vector.txt" 2021-09-25 18:33:38,616 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-25 18:33:38,616 INFO Vector2HiC Vector: vector c-tale_normalization chr5 20000 BP 2021-09-25 18:33:38,670 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpv2x4kjqw/inter.hic" "/tmp/tmpv2x4kjqw/vector.txt" 2021-09-25 18:33:42,519 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-25 18:33:42,519 INFO Vector2HiC Vector: vector c-tale_normalization chr5 25000 BP 2021-09-25 18:33:42,520 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpv2x4kjqw/inter.hic" "/tmp/tmpv2x4kjqw/vector.txt" 2021-09-25 18:33:46,496 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-25 18:33:46,496 INFO Vector2HiC Vector: vector c-tale_normalization chr5 50000 BP 2021-09-25 18:33:46,496 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpv2x4kjqw/inter.hic" "/tmp/tmpv2x4kjqw/vector.txt" 2021-09-25 18:33:50,405 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-25 18:33:50,405 DEBUG SimpleSubprocess cp "/tmp/tmpv2x4kjqw/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_norm.hic" 2021-09-25 18:33:50,802 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 18:33:50,890 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/merged_nodups.txt" 2021-09-25 18:36:04,651 INFO SimpleSubprocess CopyResult - 0:02:13 2021-09-25 18:36:04,717 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter.pairs.txt" 2021-09-25 18:36:25,611 INFO SimpleSubprocess CopyResult - 0:00:20 2021-09-25 18:36:25,611 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/vector.txt" 2021-09-25 18:36:25,642 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:25,642 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter.hic" 2021-09-25 18:36:32,552 INFO SimpleSubprocess CopyResult - 0:00:06 2021-09-25 18:36:32,553 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_statistics.txt" 2021-09-25 18:36:32,562 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:32,562 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_no_balanced_5kb.cool" 2021-09-25 18:36:33,433 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:33,433 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_5kb.cool" 2021-09-25 18:36:35,174 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-25 18:36:35,174 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_no_balanced_10kb.cool" 2021-09-25 18:36:35,426 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:35,427 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_10kb.cool" 2021-09-25 18:36:35,975 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:35,976 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_no_balanced_20kb.cool" 2021-09-25 18:36:36,827 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:36,827 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_20kb.cool" 2021-09-25 18:36:37,585 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:37,585 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_no_balanced_25kb.cool" 2021-09-25 18:36:37,772 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:37,773 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_25kb.cool" 2021-09-25 18:36:38,053 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:38,053 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_no_balanced_50kb.cool" 2021-09-25 18:36:38,994 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:38,994 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/inter_50kb.cool" 2021-09-25 18:36:39,842 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 18:36:39,910 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284499-SRR8984910/__temp__" 2021-09-25 18:37:03,645 INFO SimpleSubprocess RemoveTemp - 0:00:23 2021-09-25 18:37:03,646 INFO BenchmarkPipeline 'SRR8284499-SRR8984910' FINISHED, SUMMARY TIME - 15:27:49