2021-08-28 05:30:19,165 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179591' --- 2021-08-28 05:30:19,165 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179591.sra 2021-08-28 05:30:19,165 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__ 2021-08-28 05:30:19,166 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpsqend9yq "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179591.sra" 2021-08-28 06:10:23,698 INFO SimpleSubprocess Sra2FastQ - 0:40:04 2021-08-28 06:10:23,713 DEBUG SimpleSubprocess gzip /tmp/tmpsqend9yq/* 2021-08-28 09:39:11,413 INFO SimpleSubprocess GZipFastQ - 3:28:47 2021-08-28 09:39:11,429 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/fastq"; mv /tmp/tmpsqend9yq/SRR3179591_1.fastq.gz /tmp/tmpsqend9yq/SRR3179591_R1.fastq.gz; mv /tmp/tmpsqend9yq/SRR3179591_2.fastq.gz /tmp/tmpsqend9yq/SRR3179591_R2.fastq.gz; cp /tmp/tmpsqend9yq/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/fastq" 2021-08-28 09:44:30,022 INFO SimpleSubprocess CopyFiles - 0:05:18 2021-08-28 09:44:32,089 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__ 2021-08-28 09:44:32,089 INFO Juicer Genome assembly: mm10 2021-08-28 09:44:32,089 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-28 09:44:32,089 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 09:44:32,090 INFO Juicer Enzyme: DpnII 2021-08-28 09:44:32,090 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-28 09:44:32,090 INFO Juicer Threads: 10 2021-08-28 09:44:32,090 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/SRR3179591/__temp__" 2021-08-28 20:51:04,175 INFO SimpleSubprocess Juicer - 11:06:32 2021-08-28 20:51:04,180 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/SRR3179591/__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/SRR3179591/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/splits/SRR3179591_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/splits/SRR3179591_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/splits/SRR3179591.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/splits/SRR3179591.fastq.gz.sam done successfully (-: Finished sorting all sorted files into a single merge. WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-28T19:07:18,383] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body ........................................................................................................................................................................................................................................ Writing footer Finished preprocess Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Finished writing norms WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-28T19:47:40,855] [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/SRR3179591/__temp__/aligned/inter_30.hic. Motifs read from /Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/references/motif ARROWHEAD: WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-28T20:51:03,649] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__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/SRR3179591/__temp__/aligned for results 2021-08-28 20:51:04,231 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/merged_nodups.txt 2021-08-28 20:51:04,231 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt 2021-08-28 20:51:04,262 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpoo8uugqn/inter.pairs.txt" 2021-08-28 20:52:10,646 INFO SimpleSubprocess MakeInterPairs - 0:01:06 2021-08-28 20:52:10,646 DEBUG SimpleSubprocess cp "/tmp/tmpoo8uugqn/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt" 2021-08-28 20:52:12,323 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-28 20:52:12,548 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt 2021-08-28 20:52:12,548 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-28 20:52:12,548 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 20:52:12,548 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 20:52:12,548 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-28 20:52:12,595 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/SRR3179591/__temp__/aligned/inter.pairs.txt" "/tmp/tmp5vrt2zca/inter_no_balanced.cool" 2021-08-28 20:53:52,015 INFO SimpleSubprocess MakeCool - 0:01:39 2021-08-28 20:53:52,015 DEBUG SimpleSubprocess cp "/tmp/tmp5vrt2zca/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-28 20:53:52,069 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:53:52,073 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt 2021-08-28 20:53:52,073 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-28 20:53:52,073 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 20:53:52,073 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 20:53:52,073 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-28 20:53:52,074 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/SRR3179591/__temp__/aligned/inter.pairs.txt" "/tmp/tmpfahzd1tu/inter_no_balanced.cool" 2021-08-28 20:55:15,062 INFO SimpleSubprocess MakeCool - 0:01:22 2021-08-28 20:55:15,062 DEBUG SimpleSubprocess cp "/tmp/tmpfahzd1tu/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-28 20:55:15,088 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:55:15,092 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt 2021-08-28 20:55:15,092 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-28 20:55:15,092 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 20:55:15,092 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 20:55:15,092 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-28 20:55:15,092 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/SRR3179591/__temp__/aligned/inter.pairs.txt" "/tmp/tmpbzlt717u/inter_no_balanced.cool" 2021-08-28 20:56:33,844 INFO SimpleSubprocess MakeCool - 0:01:18 2021-08-28 20:56:33,844 DEBUG SimpleSubprocess cp "/tmp/tmpbzlt717u/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-28 20:56:33,867 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:56:33,870 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt 2021-08-28 20:56:33,870 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-28 20:56:33,870 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 20:56:33,870 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 20:56:33,870 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-28 20:56:33,891 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/SRR3179591/__temp__/aligned/inter.pairs.txt" "/tmp/tmpbjyk5_ot/inter_no_balanced.cool" 2021-08-28 20:57:54,469 INFO SimpleSubprocess MakeCool - 0:01:20 2021-08-28 20:57:54,470 DEBUG SimpleSubprocess cp "/tmp/tmpbjyk5_ot/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-28 20:57:54,491 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:57:54,494 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt 2021-08-28 20:57:54,494 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-28 20:57:54,494 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 20:57:54,494 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 20:57:54,494 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-28 20:57:54,494 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/SRR3179591/__temp__/aligned/inter.pairs.txt" "/tmp/tmpnm8axl5i/inter_no_balanced.cool" 2021-08-28 20:59:05,756 INFO SimpleSubprocess MakeCool - 0:01:11 2021-08-28 20:59:05,756 DEBUG SimpleSubprocess cp "/tmp/tmpnm8axl5i/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-28 20:59:05,773 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:59:05,796 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-28 20:59:05,796 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_5kb.cool 2021-08-28 20:59:05,797 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 20:59:05,797 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmplvf7466i/inter.cool" 2021-08-28 20:59:05,826 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 20:59:05,826 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmplvf7466i/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 20:59:11,948 INFO SimpleSubprocess NormalizeCool - 0:00:06 2021-08-28 20:59:11,948 DEBUG SimpleSubprocess cp "/tmp/tmplvf7466i/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_5kb.cool" 2021-08-28 20:59:11,978 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:59:11,982 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-28 20:59:11,982 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_10kb.cool 2021-08-28 20:59:11,982 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 20:59:11,999 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp5pi8cjk7/inter.cool" 2021-08-28 20:59:12,024 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 20:59:12,024 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp5pi8cjk7/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 20:59:15,079 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-28 20:59:15,079 DEBUG SimpleSubprocess cp "/tmp/tmp5pi8cjk7/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_10kb.cool" 2021-08-28 20:59:15,104 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:59:15,107 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-28 20:59:15,107 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_20kb.cool 2021-08-28 20:59:15,107 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 20:59:15,139 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpsfia973s/inter.cool" 2021-08-28 20:59:15,160 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 20:59:15,161 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpsfia973s/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 20:59:17,279 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-28 20:59:17,279 DEBUG SimpleSubprocess cp "/tmp/tmpsfia973s/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_20kb.cool" 2021-08-28 20:59:17,304 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:59:17,332 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-28 20:59:17,333 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_25kb.cool 2021-08-28 20:59:17,333 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 20:59:17,333 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpd9l3qdqz/inter.cool" 2021-08-28 20:59:17,354 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 20:59:17,355 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpd9l3qdqz/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 20:59:19,243 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-28 20:59:19,244 DEBUG SimpleSubprocess cp "/tmp/tmpd9l3qdqz/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_25kb.cool" 2021-08-28 20:59:19,264 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:59:19,266 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-28 20:59:19,266 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_50kb.cool 2021-08-28 20:59:19,267 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 20:59:19,284 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpug0973wq/inter.cool" 2021-08-28 20:59:19,300 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 20:59:19,300 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpug0973wq/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 20:59:20,603 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-28 20:59:20,604 DEBUG SimpleSubprocess cp "/tmp/tmpug0973wq/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_50kb.cool" 2021-08-28 20:59:20,620 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:59:20,643 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt 2021-08-28 20:59:20,649 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-28 20:59:20,649 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_5kb.cool 2021-08-28 20:59:20,649 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt 2021-08-28 20:59:20,649 INFO AddWeight Chromosome: chr11 2021-08-28 20:59:20,649 INFO AddWeight Resolution [bp]: 5000 2021-08-28 20:59:20,827 INFO AddWeight AddWeight successfully finished 2021-08-28 20:59:20,827 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_10kb.cool 2021-08-28 20:59:20,827 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt 2021-08-28 20:59:20,827 INFO AddWeight Chromosome: chr11 2021-08-28 20:59:20,827 INFO AddWeight Resolution [bp]: 10000 2021-08-28 20:59:20,875 INFO AddWeight AddWeight successfully finished 2021-08-28 20:59:20,876 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_20kb.cool 2021-08-28 20:59:20,876 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt 2021-08-28 20:59:20,876 INFO AddWeight Chromosome: chr11 2021-08-28 20:59:20,876 INFO AddWeight Resolution [bp]: 20000 2021-08-28 20:59:20,907 INFO AddWeight AddWeight successfully finished 2021-08-28 20:59:20,907 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_25kb.cool 2021-08-28 20:59:20,907 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt 2021-08-28 20:59:20,907 INFO AddWeight Chromosome: chr11 2021-08-28 20:59:20,907 INFO AddWeight Resolution [bp]: 25000 2021-08-28 20:59:20,935 INFO AddWeight AddWeight successfully finished 2021-08-28 20:59:20,935 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_50kb.cool 2021-08-28 20:59:20,935 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt 2021-08-28 20:59:20,935 INFO AddWeight Chromosome: chr11 2021-08-28 20:59:20,935 INFO AddWeight Resolution [bp]: 50000 2021-08-28 20:59:20,955 INFO AddWeight AddWeight successfully finished 2021-08-28 20:59:20,957 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.hic 2021-08-28 20:59:20,957 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_norm.hic 2021-08-28 20:59:20,957 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt 2021-08-28 20:59:20,957 INFO Vector2HiC Threads: 10 2021-08-28 20:59:20,992 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.hic" "/tmp/tmpok3u_o1m/inter.hic" 2021-08-28 20:59:21,274 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 20:59:21,275 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-08-28 20:59:21,276 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpok3u_o1m/inter.hic" "/tmp/tmpok3u_o1m/vector.txt" 2021-08-28 20:59:25,707 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-28 20:59:25,708 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-08-28 20:59:25,709 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpok3u_o1m/inter.hic" "/tmp/tmpok3u_o1m/vector.txt" 2021-08-28 20:59:29,593 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 20:59:29,593 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-08-28 20:59:29,594 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpok3u_o1m/inter.hic" "/tmp/tmpok3u_o1m/vector.txt" 2021-08-28 20:59:33,049 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 20:59:33,049 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-08-28 20:59:33,050 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpok3u_o1m/inter.hic" "/tmp/tmpok3u_o1m/vector.txt" 2021-08-28 20:59:36,718 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 20:59:36,718 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-08-28 20:59:36,719 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpok3u_o1m/inter.hic" "/tmp/tmpok3u_o1m/vector.txt" 2021-08-28 20:59:40,368 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 20:59:40,368 DEBUG SimpleSubprocess cp "/tmp/tmpok3u_o1m/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_norm.hic" 2021-08-28 20:59:40,721 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 20:59:41,475 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/merged_nodups.txt" 2021-08-28 21:01:13,420 INFO SimpleSubprocess CopyResult - 0:01:31 2021-08-28 21:01:13,420 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter.pairs.txt" 2021-08-28 21:01:25,875 INFO SimpleSubprocess CopyResult - 0:00:12 2021-08-28 21:01:25,875 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/vector.txt" 2021-08-28 21:01:26,073 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:26,073 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter.hic" 2021-08-28 21:01:29,695 INFO SimpleSubprocess CopyResult - 0:00:03 2021-08-28 21:01:29,696 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_statistics.txt" 2021-08-28 21:01:29,703 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:29,704 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_no_balanced_5kb.cool" 2021-08-28 21:01:29,886 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:29,887 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_5kb.cool" 2021-08-28 21:01:30,326 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:30,326 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_no_balanced_10kb.cool" 2021-08-28 21:01:30,525 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:30,525 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_10kb.cool" 2021-08-28 21:01:30,798 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:30,798 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_no_balanced_20kb.cool" 2021-08-28 21:01:31,310 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:31,310 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_20kb.cool" 2021-08-28 21:01:31,541 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:31,542 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_no_balanced_25kb.cool" 2021-08-28 21:01:31,756 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:31,756 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_25kb.cool" 2021-08-28 21:01:31,916 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:31,917 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_no_balanced_50kb.cool" 2021-08-28 21:01:32,096 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:32,096 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/inter_50kb.cool" 2021-08-28 21:01:32,318 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 21:01:32,393 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__" 2021-08-28 21:01:52,588 INFO SimpleSubprocess RemoveTemp - 0:00:20 2021-08-28 21:01:52,589 INFO BenchmarkPipeline 'SRR3179591' FINISHED, SUMMARY TIME - 15:31:33 2021-09-01 12:23:13,319 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179591' --- 2021-09-01 12:23:13,336 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__" 2021-09-01 12:23:13,345 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,346 INFO BenchmarkPipeline 'SRR3179591' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,799 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179591' --- 2021-09-02 13:38:17,799 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179591/__temp__" 2021-09-02 13:38:17,804 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,804 INFO BenchmarkPipeline 'SRR3179591' FINISHED, SUMMARY TIME - 0:00:00