2021-09-29 06:00:37,330 INFO BenchmarkPipeline --- START PROCESSING 'SRR8453403-SRR8453404' --- 2021-09-29 06:00:37,330 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453403.sra 2021-09-29 06:00:37,330 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__ 2021-09-29 06:00:37,330 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp5b5bpqo1 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453403.sra" 2021-09-29 06:07:05,420 INFO SimpleSubprocess Sra2FastQ - 0:06:28 2021-09-29 06:07:05,421 DEBUG SimpleSubprocess gzip /tmp/tmp5b5bpqo1/* 2021-09-29 06:22:14,120 INFO SimpleSubprocess GZipFastQ - 0:15:08 2021-09-29 06:22:14,121 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/fastq"; mv /tmp/tmp5b5bpqo1/SRR8453403_1.fastq.gz /tmp/tmp5b5bpqo1/SRR8453403_R1.fastq.gz; mv /tmp/tmp5b5bpqo1/SRR8453403_2.fastq.gz /tmp/tmp5b5bpqo1/SRR8453403_R2.fastq.gz; cp /tmp/tmp5b5bpqo1/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/fastq" 2021-09-29 06:22:16,939 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-29 06:22:17,316 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453404.sra 2021-09-29 06:22:17,316 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__ 2021-09-29 06:22:17,316 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp1d1y9fex "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453404.sra" 2021-09-29 06:42:25,088 INFO SimpleSubprocess Sra2FastQ - 0:20:07 2021-09-29 06:42:25,127 DEBUG SimpleSubprocess gzip /tmp/tmp1d1y9fex/* 2021-09-29 07:31:08,893 INFO SimpleSubprocess GZipFastQ - 0:48:43 2021-09-29 07:31:08,893 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/fastq"; mv /tmp/tmp1d1y9fex/SRR8453404_1.fastq.gz /tmp/tmp1d1y9fex/SRR8453404_R1.fastq.gz; mv /tmp/tmp1d1y9fex/SRR8453404_2.fastq.gz /tmp/tmp1d1y9fex/SRR8453404_R2.fastq.gz; cp /tmp/tmp1d1y9fex/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/fastq" 2021-09-29 07:31:21,653 INFO SimpleSubprocess CopyFiles - 0:00:12 2021-09-29 07:31:22,981 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__ 2021-09-29 07:31:22,982 INFO Juicer Genome assembly: mm10 2021-09-29 07:31:22,982 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-29 07:31:22,982 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 07:31:22,982 INFO Juicer Enzyme: DpnII 2021-09-29 07:31:22,982 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-29 07:31:22,982 INFO Juicer Threads: 10 2021-09-29 07:31:22,982 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/HIC_tmp" 2021-09-29 07:31:23,033 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-29 07:31:23,034 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/SRR8453403-SRR8453404/__temp__" 2021-09-29 15:25:26,770 INFO SimpleSubprocess Juicer - 7:54:03 2021-09-29 15:25:26,784 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/SRR8453403-SRR8453404/__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/SRR8453403-SRR8453404/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453403_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453403_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453403.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453403.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453404_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453404_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453404.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/splits/SRR8453404.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 [2021-09-29T14:05:55,498] [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 [2021-09-29T14:51:58,393] [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/SRR8453403-SRR8453404/__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 [2021-09-29T15:25:26,381] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__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/SRR8453403-SRR8453404/__temp__/aligned for results 2021-09-29 15:25:26,832 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/merged_nodups.txt 2021-09-29 15:25:26,832 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt 2021-09-29 15:25:26,832 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpg40gp2qz/inter.pairs.txt" 2021-09-29 15:27:13,022 INFO SimpleSubprocess MakeInterPairs - 0:01:46 2021-09-29 15:27:13,022 DEBUG SimpleSubprocess cp "/tmp/tmpg40gp2qz/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt" 2021-09-29 15:27:15,611 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-29 15:27:16,006 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt 2021-09-29 15:27:16,006 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-29 15:27:16,007 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 15:27:16,007 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 15:27:16,007 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-29 15:27:16,007 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/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt" "/tmp/tmp0700tt8m/inter_no_balanced.cool" 2021-09-29 15:29:44,706 INFO SimpleSubprocess MakeCool - 0:02:28 2021-09-29 15:29:44,706 DEBUG SimpleSubprocess cp "/tmp/tmp0700tt8m/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-29 15:29:44,758 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:29:44,765 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt 2021-09-29 15:29:44,765 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-29 15:29:44,765 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 15:29:44,765 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 15:29:44,765 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-29 15:29:44,789 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/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt" "/tmp/tmpdmil_89g/inter_no_balanced.cool" 2021-09-29 15:32:07,625 INFO SimpleSubprocess MakeCool - 0:02:22 2021-09-29 15:32:07,625 DEBUG SimpleSubprocess cp "/tmp/tmpdmil_89g/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-29 15:32:07,668 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:32:07,673 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt 2021-09-29 15:32:07,673 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-29 15:32:07,674 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 15:32:07,674 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 15:32:07,674 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-29 15:32:07,674 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/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2qt4sn8_/inter_no_balanced.cool" 2021-09-29 15:34:23,942 INFO SimpleSubprocess MakeCool - 0:02:16 2021-09-29 15:34:23,943 DEBUG SimpleSubprocess cp "/tmp/tmp2qt4sn8_/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-29 15:34:23,982 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:34:24,010 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt 2021-09-29 15:34:24,010 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-29 15:34:24,010 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 15:34:24,010 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 15:34:24,010 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-29 15:34:24,010 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/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt" "/tmp/tmp67qc2xkg/inter_no_balanced.cool" 2021-09-29 15:36:34,810 INFO SimpleSubprocess MakeCool - 0:02:10 2021-09-29 15:36:34,811 DEBUG SimpleSubprocess cp "/tmp/tmp67qc2xkg/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-29 15:36:34,846 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:36:34,851 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt 2021-09-29 15:36:34,851 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-29 15:36:34,851 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 15:36:34,851 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 15:36:34,851 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-29 15:36:34,851 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/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt" "/tmp/tmpuwhjrt1p/inter_no_balanced.cool" 2021-09-29 15:38:44,844 INFO SimpleSubprocess MakeCool - 0:02:09 2021-09-29 15:38:44,844 DEBUG SimpleSubprocess cp "/tmp/tmpuwhjrt1p/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-29 15:38:44,903 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:38:44,957 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-29 15:38:44,957 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_5kb.cool 2021-09-29 15:38:44,957 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 15:38:44,958 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp9qqkdsks/inter.cool" 2021-09-29 15:38:45,007 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 15:38:45,007 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp9qqkdsks/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 15:38:52,313 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-29 15:38:52,313 DEBUG SimpleSubprocess cp "/tmp/tmp9qqkdsks/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_5kb.cool" 2021-09-29 15:38:52,368 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:38:52,619 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-29 15:38:52,620 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_10kb.cool 2021-09-29 15:38:52,620 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 15:38:52,620 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpfj0sw3j5/inter.cool" 2021-09-29 15:38:52,665 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 15:38:52,665 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpfj0sw3j5/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 15:38:55,604 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-29 15:38:55,604 DEBUG SimpleSubprocess cp "/tmp/tmpfj0sw3j5/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_10kb.cool" 2021-09-29 15:38:55,652 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:38:55,688 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-29 15:38:55,688 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_20kb.cool 2021-09-29 15:38:55,688 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 15:38:55,710 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp7h51n2r2/inter.cool" 2021-09-29 15:38:55,747 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 15:38:55,747 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp7h51n2r2/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 15:38:57,936 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-29 15:38:57,937 DEBUG SimpleSubprocess cp "/tmp/tmp7h51n2r2/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_20kb.cool" 2021-09-29 15:38:57,975 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:38:58,003 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-29 15:38:58,003 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_25kb.cool 2021-09-29 15:38:58,003 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 15:38:58,003 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp0bjauzoc/inter.cool" 2021-09-29 15:38:58,041 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 15:38:58,041 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp0bjauzoc/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 15:39:00,068 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-29 15:39:00,068 DEBUG SimpleSubprocess cp "/tmp/tmp0bjauzoc/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_25kb.cool" 2021-09-29 15:39:00,109 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:39:00,115 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-29 15:39:00,115 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_50kb.cool 2021-09-29 15:39:00,115 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 15:39:00,141 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpv6en5xgr/inter.cool" 2021-09-29 15:39:00,174 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 15:39:00,174 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpv6en5xgr/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 15:39:01,567 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-29 15:39:01,567 DEBUG SimpleSubprocess cp "/tmp/tmpv6en5xgr/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_50kb.cool" 2021-09-29 15:39:01,599 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:39:01,605 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt 2021-09-29 15:39:01,612 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-29 15:39:01,613 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_5kb.cool 2021-09-29 15:39:01,613 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt 2021-09-29 15:39:01,613 INFO AddWeight Chromosome: chr11 2021-09-29 15:39:01,613 INFO AddWeight Resolution [bp]: 5000 2021-09-29 15:39:01,703 INFO AddWeight AddWeight successfully finished 2021-09-29 15:39:01,704 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_10kb.cool 2021-09-29 15:39:01,704 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt 2021-09-29 15:39:01,704 INFO AddWeight Chromosome: chr11 2021-09-29 15:39:01,704 INFO AddWeight Resolution [bp]: 10000 2021-09-29 15:39:01,754 INFO AddWeight AddWeight successfully finished 2021-09-29 15:39:01,754 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_20kb.cool 2021-09-29 15:39:01,754 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt 2021-09-29 15:39:01,754 INFO AddWeight Chromosome: chr11 2021-09-29 15:39:01,754 INFO AddWeight Resolution [bp]: 20000 2021-09-29 15:39:01,787 INFO AddWeight AddWeight successfully finished 2021-09-29 15:39:01,787 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_25kb.cool 2021-09-29 15:39:01,788 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt 2021-09-29 15:39:01,788 INFO AddWeight Chromosome: chr11 2021-09-29 15:39:01,788 INFO AddWeight Resolution [bp]: 25000 2021-09-29 15:39:01,817 INFO AddWeight AddWeight successfully finished 2021-09-29 15:39:01,817 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_50kb.cool 2021-09-29 15:39:01,817 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt 2021-09-29 15:39:01,817 INFO AddWeight Chromosome: chr11 2021-09-29 15:39:01,817 INFO AddWeight Resolution [bp]: 50000 2021-09-29 15:39:01,839 INFO AddWeight AddWeight successfully finished 2021-09-29 15:39:01,841 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.hic 2021-09-29 15:39:01,841 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_norm.hic 2021-09-29 15:39:01,841 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt 2021-09-29 15:39:01,841 INFO Vector2HiC Threads: 10 2021-09-29 15:39:01,861 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.hic" "/tmp/tmpixeecmyj/inter.hic" 2021-09-29 15:39:02,635 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 15:39:02,635 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-09-29 15:39:02,637 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpixeecmyj/inter.hic" "/tmp/tmpixeecmyj/vector.txt" 2021-09-29 15:39:07,770 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-29 15:39:07,771 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-09-29 15:39:07,772 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpixeecmyj/inter.hic" "/tmp/tmpixeecmyj/vector.txt" 2021-09-29 15:39:12,072 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 15:39:12,072 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-09-29 15:39:12,073 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpixeecmyj/inter.hic" "/tmp/tmpixeecmyj/vector.txt" 2021-09-29 15:39:16,171 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 15:39:16,171 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-09-29 15:39:16,172 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpixeecmyj/inter.hic" "/tmp/tmpixeecmyj/vector.txt" 2021-09-29 15:39:20,464 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 15:39:20,465 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-09-29 15:39:20,468 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpixeecmyj/inter.hic" "/tmp/tmpixeecmyj/vector.txt" 2021-09-29 15:39:24,843 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 15:39:24,844 DEBUG SimpleSubprocess cp "/tmp/tmpixeecmyj/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_norm.hic" 2021-09-29 15:39:25,289 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 15:39:25,785 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/merged_nodups.txt" 2021-09-29 15:41:16,531 INFO SimpleSubprocess CopyResult - 0:01:50 2021-09-29 15:41:16,531 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter.pairs.txt" 2021-09-29 15:41:46,767 INFO SimpleSubprocess CopyResult - 0:00:30 2021-09-29 15:41:46,792 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/vector.txt" 2021-09-29 15:41:46,876 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:46,876 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter.hic" 2021-09-29 15:41:53,525 INFO SimpleSubprocess CopyResult - 0:00:06 2021-09-29 15:41:53,526 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_statistics.txt" 2021-09-29 15:41:53,533 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:53,534 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_no_balanced_5kb.cool" 2021-09-29 15:41:54,389 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:54,389 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_5kb.cool" 2021-09-29 15:41:54,986 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:54,987 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_no_balanced_10kb.cool" 2021-09-29 15:41:55,566 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:55,566 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_10kb.cool" 2021-09-29 15:41:56,253 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:56,253 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_no_balanced_20kb.cool" 2021-09-29 15:41:56,747 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:56,747 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_20kb.cool" 2021-09-29 15:41:57,238 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:57,238 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_no_balanced_25kb.cool" 2021-09-29 15:41:57,824 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:57,824 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_25kb.cool" 2021-09-29 15:41:58,561 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:58,561 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_no_balanced_50kb.cool" 2021-09-29 15:41:58,783 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:58,783 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/inter_50kb.cool" 2021-09-29 15:41:58,993 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 15:41:59,216 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453403-SRR8453404/__temp__" 2021-09-29 15:42:08,105 INFO SimpleSubprocess RemoveTemp - 0:00:08 2021-09-29 15:42:08,105 INFO BenchmarkPipeline 'SRR8453403-SRR8453404' FINISHED, SUMMARY TIME - 9:41:30