2021-08-27 16:01:06,382 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179590' --- 2021-08-27 16:01:06,382 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179590.sra 2021-08-27 16:01:06,382 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__ 2021-08-27 16:01:06,494 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpfl65ydnh "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3179590.sra" 2021-08-27 16:43:13,631 INFO SimpleSubprocess Sra2FastQ - 0:42:07 2021-08-27 16:43:13,645 DEBUG SimpleSubprocess gzip /tmp/tmpfl65ydnh/* 2021-08-27 19:32:24,288 INFO SimpleSubprocess GZipFastQ - 2:49:10 2021-08-27 19:32:24,322 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/fastq"; mv /tmp/tmpfl65ydnh/SRR3179590_2.fastq.gz /tmp/tmpfl65ydnh/SRR3179590_R2.fastq.gz; mv /tmp/tmpfl65ydnh/SRR3179590_1.fastq.gz /tmp/tmpfl65ydnh/SRR3179590_R1.fastq.gz; cp /tmp/tmpfl65ydnh/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/fastq" 2021-08-27 19:38:12,967 INFO SimpleSubprocess CopyFiles - 0:05:48 2021-08-27 19:38:14,718 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__ 2021-08-27 19:38:14,718 INFO Juicer Genome assembly: mm10 2021-08-27 19:38:14,718 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-27 19:38:14,718 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-27 19:38:14,718 INFO Juicer Enzyme: DpnII 2021-08-27 19:38:14,718 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-27 19:38:14,719 INFO Juicer Threads: 10 2021-08-27 19:38:14,719 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/SRR3179590/__temp__" 2021-08-28 05:20:02,889 INFO SimpleSubprocess Juicer - 9:41:48 2021-08-28 05:20:02,955 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/SRR3179590/__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/SRR3179590/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/splits/SRR3179590_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/splits/SRR3179590_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/splits/SRR3179590.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/splits/SRR3179590.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 [2021-08-28T04:10:04,121] [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 [2021-08-28T04:50:49,627] [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/SRR3179590/__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 [2021-08-28T05:20:02,005] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__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/SRR3179590/__temp__/aligned for results 2021-08-28 05:20:03,056 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/merged_nodups.txt 2021-08-28 05:20:03,056 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt 2021-08-28 05:20:03,062 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpxbpapp6e/inter.pairs.txt" 2021-08-28 05:21:06,375 INFO SimpleSubprocess MakeInterPairs - 0:01:03 2021-08-28 05:21:06,375 DEBUG SimpleSubprocess cp "/tmp/tmpxbpapp6e/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt" 2021-08-28 05:21:07,916 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-28 05:21:08,759 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt 2021-08-28 05:21:08,760 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-28 05:21:08,760 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 05:21:08,760 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 05:21:08,760 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-28 05:21:08,783 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/SRR3179590/__temp__/aligned/inter.pairs.txt" "/tmp/tmpfyr4exvk/inter_no_balanced.cool" 2021-08-28 05:22:36,782 INFO SimpleSubprocess MakeCool - 0:01:27 2021-08-28 05:22:36,782 DEBUG SimpleSubprocess cp "/tmp/tmpfyr4exvk/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-28 05:22:36,830 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:22:36,833 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt 2021-08-28 05:22:36,833 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-28 05:22:36,834 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 05:22:36,834 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 05:22:36,834 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-28 05:22:36,834 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/SRR3179590/__temp__/aligned/inter.pairs.txt" "/tmp/tmpeuw7kafg/inter_no_balanced.cool" 2021-08-28 05:23:55,245 INFO SimpleSubprocess MakeCool - 0:01:18 2021-08-28 05:23:55,245 DEBUG SimpleSubprocess cp "/tmp/tmpeuw7kafg/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-28 05:23:55,268 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:23:55,270 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt 2021-08-28 05:23:55,270 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-28 05:23:55,271 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 05:23:55,271 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 05:23:55,271 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-28 05:23:55,289 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/SRR3179590/__temp__/aligned/inter.pairs.txt" "/tmp/tmpsbwuo2o5/inter_no_balanced.cool" 2021-08-28 05:25:09,043 INFO SimpleSubprocess MakeCool - 0:01:13 2021-08-28 05:25:09,043 DEBUG SimpleSubprocess cp "/tmp/tmpsbwuo2o5/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-28 05:25:09,063 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:25:09,085 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt 2021-08-28 05:25:09,085 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-28 05:25:09,085 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 05:25:09,085 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 05:25:09,086 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-28 05:25:09,086 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/SRR3179590/__temp__/aligned/inter.pairs.txt" "/tmp/tmpx507yqad/inter_no_balanced.cool" 2021-08-28 05:26:21,092 INFO SimpleSubprocess MakeCool - 0:01:12 2021-08-28 05:26:21,092 DEBUG SimpleSubprocess cp "/tmp/tmpx507yqad/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-28 05:26:21,111 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:26:21,138 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt 2021-08-28 05:26:21,138 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-28 05:26:21,138 INFO Pairs2Cool Genome assembly: mm10 2021-08-28 05:26:21,138 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-28 05:26:21,138 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-28 05:26:21,158 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/SRR3179590/__temp__/aligned/inter.pairs.txt" "/tmp/tmp7w5wy6vl/inter_no_balanced.cool" 2021-08-28 05:27:30,503 INFO SimpleSubprocess MakeCool - 0:01:09 2021-08-28 05:27:30,504 DEBUG SimpleSubprocess cp "/tmp/tmp7w5wy6vl/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-28 05:27:30,520 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:27:30,523 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-28 05:27:30,523 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_5kb.cool 2021-08-28 05:27:30,524 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 05:27:30,524 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpvipusmxz/inter.cool" 2021-08-28 05:27:30,551 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 05:27:30,551 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpvipusmxz/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 05:27:35,653 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-08-28 05:27:35,654 DEBUG SimpleSubprocess cp "/tmp/tmpvipusmxz/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_5kb.cool" 2021-08-28 05:27:35,787 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:27:35,991 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-28 05:27:35,991 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_10kb.cool 2021-08-28 05:27:35,991 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 05:27:36,016 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpjqk294ig/inter.cool" 2021-08-28 05:27:36,041 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 05:27:36,041 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpjqk294ig/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 05:27:38,592 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-28 05:27:38,593 DEBUG SimpleSubprocess cp "/tmp/tmpjqk294ig/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_10kb.cool" 2021-08-28 05:27:38,615 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:27:38,618 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-28 05:27:38,618 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_20kb.cool 2021-08-28 05:27:38,618 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 05:27:38,619 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpzk8pc_7r/inter.cool" 2021-08-28 05:27:38,638 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 05:27:38,639 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpzk8pc_7r/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 05:27:40,528 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-28 05:27:40,528 DEBUG SimpleSubprocess cp "/tmp/tmpzk8pc_7r/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_20kb.cool" 2021-08-28 05:27:40,548 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:27:40,558 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-28 05:27:40,558 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_25kb.cool 2021-08-28 05:27:40,558 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 05:27:40,588 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpr_el_k8_/inter.cool" 2021-08-28 05:27:40,607 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 05:27:40,607 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpr_el_k8_/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 05:27:42,297 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-28 05:27:42,297 DEBUG SimpleSubprocess cp "/tmp/tmpr_el_k8_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_25kb.cool" 2021-08-28 05:27:42,316 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:27:42,318 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-28 05:27:42,318 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_50kb.cool 2021-08-28 05:27:42,318 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-28 05:27:42,319 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpczaqw5se/inter.cool" 2021-08-28 05:27:42,335 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 05:27:42,335 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpczaqw5se/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-28 05:27:43,580 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-28 05:27:43,580 DEBUG SimpleSubprocess cp "/tmp/tmpczaqw5se/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_50kb.cool" 2021-08-28 05:27:43,598 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:27:43,621 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt 2021-08-28 05:27:43,627 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-28 05:27:43,628 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_5kb.cool 2021-08-28 05:27:43,628 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt 2021-08-28 05:27:43,628 INFO AddWeight Chromosome: chr11 2021-08-28 05:27:43,628 INFO AddWeight Resolution [bp]: 5000 2021-08-28 05:27:44,576 INFO AddWeight AddWeight successfully finished 2021-08-28 05:27:44,576 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_10kb.cool 2021-08-28 05:27:44,576 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt 2021-08-28 05:27:44,576 INFO AddWeight Chromosome: chr11 2021-08-28 05:27:44,576 INFO AddWeight Resolution [bp]: 10000 2021-08-28 05:27:44,625 INFO AddWeight AddWeight successfully finished 2021-08-28 05:27:44,625 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_20kb.cool 2021-08-28 05:27:44,625 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt 2021-08-28 05:27:44,625 INFO AddWeight Chromosome: chr11 2021-08-28 05:27:44,625 INFO AddWeight Resolution [bp]: 20000 2021-08-28 05:27:44,656 INFO AddWeight AddWeight successfully finished 2021-08-28 05:27:44,656 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_25kb.cool 2021-08-28 05:27:44,657 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt 2021-08-28 05:27:44,657 INFO AddWeight Chromosome: chr11 2021-08-28 05:27:44,657 INFO AddWeight Resolution [bp]: 25000 2021-08-28 05:27:44,684 INFO AddWeight AddWeight successfully finished 2021-08-28 05:27:44,684 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_50kb.cool 2021-08-28 05:27:44,684 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt 2021-08-28 05:27:44,684 INFO AddWeight Chromosome: chr11 2021-08-28 05:27:44,684 INFO AddWeight Resolution [bp]: 50000 2021-08-28 05:27:44,705 INFO AddWeight AddWeight successfully finished 2021-08-28 05:27:44,707 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.hic 2021-08-28 05:27:44,707 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_norm.hic 2021-08-28 05:27:44,707 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt 2021-08-28 05:27:44,707 INFO Vector2HiC Threads: 10 2021-08-28 05:27:44,726 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.hic" "/tmp/tmp9wodma6u/inter.hic" 2021-08-28 05:27:45,000 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-28 05:27:45,000 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-08-28 05:27:45,002 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp9wodma6u/inter.hic" "/tmp/tmp9wodma6u/vector.txt" 2021-08-28 05:27:49,405 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-28 05:27:49,405 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-08-28 05:27:49,406 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp9wodma6u/inter.hic" "/tmp/tmp9wodma6u/vector.txt" 2021-08-28 05:27:53,268 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 05:27:53,268 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-08-28 05:27:53,269 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp9wodma6u/inter.hic" "/tmp/tmp9wodma6u/vector.txt" 2021-08-28 05:27:56,794 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 05:27:56,794 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-08-28 05:27:56,795 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp9wodma6u/inter.hic" "/tmp/tmp9wodma6u/vector.txt" 2021-08-28 05:28:00,554 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 05:28:00,554 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-08-28 05:28:00,555 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp9wodma6u/inter.hic" "/tmp/tmp9wodma6u/vector.txt" 2021-08-28 05:28:04,271 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-28 05:28:04,272 DEBUG SimpleSubprocess cp "/tmp/tmp9wodma6u/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_norm.hic" 2021-08-28 05:28:04,614 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-28 05:28:05,746 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/merged_nodups.txt" 2021-08-28 05:29:44,109 INFO SimpleSubprocess CopyResult - 0:01:38 2021-08-28 05:29:44,109 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter.pairs.txt" 2021-08-28 05:29:56,164 INFO SimpleSubprocess CopyResult - 0:00:12 2021-08-28 05:29:56,164 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/vector.txt" 2021-08-28 05:29:56,172 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:29:56,172 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter.hic" 2021-08-28 05:29:59,687 INFO SimpleSubprocess CopyResult - 0:00:03 2021-08-28 05:29:59,687 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_statistics.txt" 2021-08-28 05:29:59,694 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:29:59,695 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_no_balanced_5kb.cool" 2021-08-28 05:29:59,888 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:29:59,888 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_5kb.cool" 2021-08-28 05:30:00,080 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,080 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_no_balanced_10kb.cool" 2021-08-28 05:30:00,224 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,224 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_10kb.cool" 2021-08-28 05:30:00,371 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,372 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_no_balanced_20kb.cool" 2021-08-28 05:30:00,492 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,492 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_20kb.cool" 2021-08-28 05:30:00,612 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,613 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_no_balanced_25kb.cool" 2021-08-28 05:30:00,731 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,731 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_25kb.cool" 2021-08-28 05:30:00,829 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,829 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_no_balanced_50kb.cool" 2021-08-28 05:30:00,904 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:00,904 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/inter_50kb.cool" 2021-08-28 05:30:00,999 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-28 05:30:01,096 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__" 2021-08-28 05:30:18,930 INFO SimpleSubprocess RemoveTemp - 0:00:17 2021-08-28 05:30:18,930 INFO BenchmarkPipeline 'SRR3179590' FINISHED, SUMMARY TIME - 13:29:12 2021-09-01 12:23:13,294 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179590' --- 2021-09-01 12:23:13,309 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__" 2021-09-01 12:23:13,318 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,318 INFO BenchmarkPipeline 'SRR3179590' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,791 INFO BenchmarkPipeline --- START PROCESSING 'SRR3179590' --- 2021-09-02 13:38:17,791 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3179590/__temp__" 2021-09-02 13:38:17,798 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,798 INFO BenchmarkPipeline 'SRR3179590' FINISHED, SUMMARY TIME - 0:00:00